gebhart/patrepeval huggingface dataset:
Simulation of Tunneling in Enzyme Catalysis by Combining a Biased Propagation Approach and the Quantum Classical Path Method:  Application to Lipoxygenase (2007)

The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.
The innate immune response of the respiratory epithelium (2000)

The respiratory epithelium maintains an effective antimicrobial environment to prevent colonization by microorganisms in inspired air. In addition to constitutively present host defenses which include antimicrobial peptides and proteins, the epithelial cells respond to the presence of microbes by the induction two complementary parts of an innate immune response. The first response is the increased production of antimicrobial agents, and the second is the induction of a signal network to recruit phagocytic cells to contain the infection. Inflammatory mediators released by the recruited cells as well as from the epithelium itself further induce the expression of the antimicrobial agents. The result is an effective prevention of microbial colonization. The epithelial cells recognize the pathogen-associated patterns on microbes by surface receptors such as CD14 and Toll-like receptors. Subsequent signal transduction pathways have been identified which result in the increased transcription of host defense response genes. Diseases such as cystic fibrosis, or environmental exposures such as the inhalation of air pollution particles, may create an environment that impairs the expression or activity of the host defenses in the airway. This can lead to increased susceptibility to airway infections.
Minimum Infective Dose of Mycobacterium bovis in Cattle (2005)

The aim of this work was to determine the minimum infective dose of Mycobacterium bovis necessary to stimulate specific immune responses and generate pathology in cattle. Four groups of calves (20 animals) were infected by the intratracheal route with 1,000, 100, 10, or 1 CFU of M. bovis. Specific immune responses (gamma interferon [IFN-gamma] and interleukin-4 [IL-4] responses) to mycobacterial antigens were monitored throughout the study, and the responses to the tuberculin skin test were assessed at two times. Rigorous post mortem examinations were performed to determine the presence of pathology, and samples were taken for microbiological and histopathological confirmation of M. bovis infection. One-half of the animals infected with 1 CFU of M. bovis developed pulmonary pathology typical of bovine tuberculosis. No differences in the severity of pathology were observed for the different M. bovis doses. All animals that developed pathology were skin test positive and produced specific IFN-gamma and IL-4 responses. No differences in the sizes of the skin test reactions, the times taken to achieve a positive IFN-gamma result, or the levels of the IFN-gamma and IL-4 responses were observed for the different M. bovis doses, suggesting that diagnostic assays (tuberculin skin test and IFN-gamma test) can detect cattle soon after M. bovis infection regardless of the dose. This information should be useful in modeling the dynamics of bovine tuberculosis in cattle and in assessing the risk of transmission.
Analysis of the Machining Process Using a Thermo-Elastic-Viscoplastic Finite Element Model (2002)

A plane-strain thermo-elasto-viscoplastic finite element model has been developed and used to simulate orthogonal machining. Simulations of cutting 304L stainless steel have been carried out using sharp, chamfered, and honed ceramic tools. Employing a combined thermal and mechanical stress analysis with temperature-dependent physical properties, the finite element model is used to investigate the effect of process parameters, tool geometry and edge preparation on the machining process. Stress and strain distributions within the chip and the elastic tool are presented. In addition, trends in the cutting and thrust forces, contact stress distributions and the plastic deformation beneath the machined surface are studied.
Railway vibration reduction using impact dampers (2014)

The use of impact dampers for reducing railway vibration induced from moving wheel loads and consequent noise generation is presented. The impact dampers for efficient reduction of impact vibration induced by moving loads were designed and verified using simple dynamic models. To test the performance of the impact dampers, the vibration of a simplified beam attached with various impact dampers was measured. The performance of the impact damper on reducing the transient vibration of railway is investigated. The effects of clearance and mass ratio on vibration reduction was analyzed. The numerical solutions using finite element method were verified using the experimental results to find the vibration reduction mechanism. The result was utilized to reduce rolling noise radiation from moving trains.
Proposed Host-Front End Protocol (1984)

The reader should be aware of several things in regard to what the present document is up to. First and foremost, IT IS A PROPOSAL FOR A STANDARD, NOT A STANDARD ITSELF. Next, it assumes that the separate document, RFC 928, which is an introduction to the present document, has been read before it is. Next, it should be understood that &amp;quot;final cut &amp;quot; over this version of the document has been exercised by the author of RFC 928, not by the primary author of the present document, so any readers bothered by style considerations should feel free to blame the former, who’s used to it, rather than the latter, who may well be guiltless. (Editing at a distance finally become too hard to manage, so if I’m typing it myself I’m going to fiddle with it myself too, including, but not limited to, sticking my own section on the Conceptual Model in before Joel’s words start, rather than leaving it in the Introduction. MAP) Finally, it should be noted that this is not a finished document.
Restriction of primary responses to the IgG class and dependency of IgM responses on secondary immunization for the copolymers of L-glutamic acid, L-tyrosine, and L-alanine. (1977)

Primary responses to the linear polymers of L-glutamic acid, L-tyrosine, and L-alanine are restricted to the IgG class of antibodies. The appearance of specific IgM antibodies against these antigens is dependent upon secondary immunization, in contrast to many classical antigenic systems. The presence of an IgM response was verified by a direct plaque-forming cell assay, the inhibition of direct plaques by an antiserum specific for mouse micron-chain, and the physical separation of IgM and IgG GAT-specific antibodies by gel filtration. Preimmunization of the appropriate nonresponder strain with GAT or GT inhibits both the secondary IgM and IgG responses to GAT-MBSA and GT-MBSA, respectively. The tolerance observed is due to the induction of suppressor cells as demonstrated by cell transfer experiments.
Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death (2011)

Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348-1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.
Trial of radiolabeled antibody localization in metastases of a patient with a tumor containing carcinoembryonic antigen (CEA) (1974)

Abstract An attempt to detect metastatic cancer by the specific localization of radiolabeled antibody is reported. The patient had far advanced carcinoma of the colon and a high level of carcinoembryonic antigen (CEA) in serum. She was given whole unabsorbed rabbit antiserum to CEA intravenously, to determine whether CEA can be removed from the circulation. A transient partial depression of the CEA level in serum was obtained, followed by a rebound. Absorbed and purified antibody radiolabeled with 131 I was injected intravenously 19 days later. Total body scans showed no evidence of the localization of the radiolabel in cancer tissue. After another 5 days, injection of the same radiolabeled antibody solution directly into the hepatic artery was attempted. Again, no evidence of localization in liver metastases was obtained. All three infusions of antibody to CEA caused reactions that were ameliorated by Benadryl. Future trials may have better Success if monospecific anti‐CEA is used and patients are chosen who have CEA‐producing tumors, but whose serum CEA levels are low or negative.
Freestanding GaN‐substrates and devices (2003)

Various physical aspects and potential applications of the laser-induced separation of GaN epilayers from their sapphire substrate are reviewed. The effect of short laser pulses on the thermal decomposition of GaN and possible applications of the laser-induced dissociation of GaN for fast etching of this material is discussed. Particular emphasis is placed on the defect-free delamination of large area GaN films with thicknesses ranging from 3 to 300 μm from sapphire substrates. The use of the resulting freestanding GaN films in device technology and homoepitaxy of III-nitrides are outlined. Specific examples are the flip-chip bonding of freestanding InGaN/GaN LEDs to a silicon submount and the production of pseudosubstrates for the homoepitaxy of high quality GaN epilayers. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
In Vitro Cell-Mediated Biomineralization Of 3D Porous Titanium Scaffolds – A Novel Biomimicry Strategy Towards Osteoinductive Carriers (2013)

In vitro cell-derived mineralized matrix deposition on scaffolds have been shown to induce in vitro osteogenic differentiation of progenitor cells, but in vivo osteoinductivity of these constructs is so far not apparent. In this study, we have developed three types of biomineralization media (BM) and studied their effect on the osteogenic differentiation and mineralized matrix deposition onto 3D open porous Ti6Al4V scaffolds by human osteoprogenitor cells (hPDCs). In a medium-dependent manner, the three BM enhanced hPDC 3D proliferation and upregulated early (Runx2) and late osteogenic differentiation (Dlx5, Osterix and osteocalcin) markers, as well as BMP2, a Wnt signaling target gene (LEF1) and vascular endothelial growth factor (VEGF) gene expression. Interestingly, the RankL/OPG ratio was also upregulated, which may indicate hPDC modulation in osteoclastogenesis and thus potential for mineralized matrix remodeling. Indeed, principle component analysis showed that the BM treatments resulted in the enrichment of distinct cell populations represented by highly upregulated specific gene clusters. By devitalization mineralized carriers were produced and used as customized delivery vehicle to implant freshly seeded hPDCs in a nude mouse ectopic bone formation model. Encouragingly, all cell-carrier combinations resulted either in bone ossicles containing bone marrow within the scaffold pores or bone formed directly on the scaffold surface. In conclusion, we have presented a novel biomimetic strategy to functionalize 3D porous scaffolds with a cell-derived mineralized matrix in a customized way that can assist the translation to effective bone defect repair.
THE ANATOMICAL BASIS OF CONDUCTION APHASIA (1980)

Journal Article THE ANATOMICAL BASIS OF CONDUCTION APHASIA Get access HANNA DAMASIO, HANNA DAMASIO Department of Neurology (Division of Behavioral Neurology and Benton Laboratory of Neuropsychology), University of Iowa College of MedicineIowa City, Iowa 52242, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar ANTONIO R. DAMASIO ANTONIO R. DAMASIO Department of Neurology (Division of Behavioral Neurology and Benton Laboratory of Neuropsychology), University of Iowa College of MedicineIowa City, Iowa 52242, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Brain, Volume 103, Issue 2, June 1980, Pages 337–350, https://doi.org/10.1093/brain/103.2.337 Published: 01 June 1980 Article history Received: 19 July 1979 Published: 01 June 1980
A Harmonic-based Fault detection algorithm for Microgrids (2023)

The trend toward Microgrids (MGs) is significantly increasing by employing Distributed Generators (DGs) which leads to new challenges, especially in the fault detection. This paper proposes an algorithm based on the Total Harmonic Distortion (THD) of the grid voltages to detect the events of faults in MGs. The algorithm uses the THD together with the estimate amplitude voltages and the zero-sequence component for the detection and identification of the faults. The performance is evaluated by using MATLAB/Simulink simulations to validate the capability for detecting different fault types in the least possible time.
A Method for Extraction of Function Modules of Sequential Control Programs Based on Structure Analysis (2007)

In this paper, a method to extract function modules from sequential control programs is proposed. A hierarchical structure of a given sequential program can be found by using association graph. If some or more variables are connected each other (strongly connected), the layered structure is not easy to find. Thus, based on the concept of Markov chain, the importance of variables can be conducted. We propose a new method to divide unclear layered variables in more details. An illustrative example of a tank control program is shown as an application of the proposed method.
Rice Transformation with Cell Wall Degrading Enzyme Genes from Trichoderma atroviride and Its Effect on Plant Growth and Resistance to Fungal Pathogens (2004)

Three genes encoding for fungal cell wall degrading enzymes (CWDE), ech42, nag70 and gluc78 from the biocontrol fungus Trichoderma atroviride were inserted into the binary vector pCAMBLA1305.2 singly and in all possible combinations. The coding sequences were placed downstream of the rice actin promoter and all vectors were used to transform rice plants. A total of more than 1,800 independently regenerated plantlets in seven different populations (for each of the three genes and each of the four gene combinations) were obtained. Expression in plant was obtained for all the fungal genes used singly or in combinations. The ech42 gene encoding for an endochitinase increased resistance to sheath blight caused by Rhizoctonia solani, while the exochitinase-encoding gene, nag70, had a lesser effect. The expression level of endochitinase but not of the exochitinase was correlated with disease resistance. Nevertheless, exochitinase enhanced the positive effect of endochitinase on disease resistance when two genes were co-expressed in transgenic rice. Improved resistance to Magnaporthe grisea was found in all types of regenerated plants, including those with the gluc78 gene alone, while a few lines expressing either ech42 or nag70 appeared to be immune to this pathogen. Transgenic plants expressing the gluc78 gene alone were stunted and only few of them survived, even though they showed resistance to M. grisea. However, combination with either one of the two other genes (ech42, nag70) as included in the same T-DNA region, reduced the negative effect of gluc78 on plant growth. This is the first report of single or multiple of expression of transgens encoding CWDEs that results in resistance to blast and sheath blight in rice.
Screening for Tumours in Paraneoplastic Syndromes (2011)

Background: Paraneoplastic neurological syndromes (PNS) almost invariably precede detection of the malignancy. Screening for tumours is important in PNS as the tumour directly affects prognosis, and treatment and should be performed as soon as possible. Objectives: An overview of the screening of tumours related to classical PNS is given. Small cell lung cancer, thymoma, breast cancer, ovarian carcinoma and teratoma, and testicular tumours are described in relation to paraneoplastic limbic encephalitis, subacute sensory neuronopathy, subacute autonomic neuropathy, paraneoplastic cerebellar degeneration, paraneoplastic opsoclonus-myoclonus, Lambert-Eaton myasthenic syndrome, myasthenia gravis and paraneoplastic peripheral nerve hyperexcitability. Methods: Many studies with class IV evidence were available; one study reached level III evidence. No evidence-based recommendations for Levels A–C were possible, but good practice points were agreed by consensus. Recommendations: The nature of the antibody, and to a lesser extent the clinical syndrome, determines the risk and type of an underlying malignancy. For screening of the thoracic region a CT thorax is recommended, which if negative is followed by FDG-PET. Breast cancer is screened for by mammography, followed by MRI. For the pelvic region ultrasound is the investigation of first choice followed by CT. Dermatomyositis patients should have CT thorax/abdomen, ultrasound (US) of the pelvic region and mammography in women, US of testes in men under 50 years and colonoscopy in men and women over 50. If primary screening is negative, repeat screening after 3–6 months and screen every 6 months for up to 4 years. In LEMS, screening for 2 years is sufficient. In syndromes where only a subgroup of patients has a malignancy, tumour markers have additional value to predict a probable malignancy.
Operation of HDLC abm in harsh error environments: a robust extension (1991)

The use of an extension to the high level data link control (HDLC) asynchronous balanced mode protocol to provide a reliable satellite data link service which is resilient, without operator intervention, in high levels of noise is described. Research has been directed toward providing a robust data link for the interconnections of stations using a communications satellite. Two mechanisms are described which protect the flow of control information. One is forward error correction of the control portion of the HDLC frames. The other is an extended protocol that employs redundant supervisory frames which are interleaved with the normal link traffic. The implementation of these schemes is outlined. The extended protocol is superior, providing tolerance to a wide range of error environments.
Valence-bond isomer chemistry. Part V. Hexafluorobicyclo[2.2.0]-hexa-2,5-diene and its derivatives as dipolarophiles (1973)

Hexafluorobicyclo[2.2.0]hexa-2,5-diene is an active dipolarophile, reacting with the representative 1,3-dipoles phenyl azide. diazomethane, 2,2,2-trifluorodiazoethane. 2,4,6-trimethylbenzonitrile oxide, and benzonitrile N-phenylimide to give 1 : 1 adducts, and mixtures of 1 : 2 adducts. Related compounds are similarly reactive, addition to the CF:CF double bond of 2-methoxypentafluorobicyclo [2.2.0]hexa-2,5-diene, and of exo-5,6-dibromohexa-fluorobicyclo [2.2.0]hex-2-ene, occurring with phenyl azide and with 2,4,6-trimethylbenzonitrile oxide, respectively. 19F N.m.r. studies indicate that reaction occurs by exo-addition to the bicyclo-compounds.The phenyl azide adducts, 1,2,3,4,5,6-hexafluoro-9-phenyl-7,8,9-triazatricyclo[4.3.0.02,5]nona-3,7-diene and 1,2,3,5,6,7-hexafluoro-4,10-diphenyl-4,8,9,10-tetra-azatetracyclo[5.3.0.02,6.03,5]dec-8-ene, lose nitrogen upon u.v. photolysis in acetone solution, to give the derived aziridines.
Energy Harvesting Wireless Sensors for Helicopter Damage Tracking (2006)

The knowledge of operational loads on a helicopter rotating components is important for condition based maintenance (CBM) and health usage monitoring systems (HUMS). In the past, the need to deploy slip rings has limited the monitoring of rotating components. Wireless technology eliminates slip rings, but the problem of battery maintenance remains a major obstacle. This paper reports on next generation wireless sensors which eliminate battery maintenance by using piezoelectric materials to convert strain energy to stored electrical energy. Stored energy is used to measure, record, and transmit strain and load information. A prototype energy harvesting wireless pitch link sensing system has been developed. Under low usage level helicopter operating conditions, the energy consumed was less than the energy harvested, enabling strain & load sensors to operate perpetually without battery maintenance. Breaking down the barriers to monitoring helicopter rotating components, this technology has the potential to greatly improve future HUMS capabilities.
Zinc-Finger Nucleases: A Panoramic View (2011)

Zinc-finger nucleases (ZFNs) are emerging as very powerful tools for directed genome modifications. Their key features are: a DNA-binding domain comprised of zinc fingers that can be designed to favor very specific targets; a nonspecific cleavage domain that must dimerize to cut DNA--this requirement enhances specificity and minimizes random cleavage. ZFNs have been shown to be effective in a wide range of organisms and cell types. This article reviews discoveries that led to the development of ZFNs, cites examples of successes in genome engineering, and projects how ZFNs may be used in the future, particularly in applications to humans.
Objective assessment of patient compliance with removable orthodontic appliances: A cross-sectional cohort study (2013)

Despite the fact that patients and parents were informed about wear time recording, compliance was insufficient with regard to functional treatment (14 h/d prescription), while it was sufficient for retention purposes (8 h/d prescription). Objective measures are necessary to assess compliance with removable orthodontic appliances since patient compliance is a highly variable issue.