gebhart/patrepeval huggingface dataset:
Ruolo della proteina arginin-metiltrasferasi-5 (PRMT5) nella linfomagenesi B: implicazioni terapeutiche (2011)

Numerosi studi hanno mostrato come i meccanismi epigenetici di regolazione della cromatina svolgano un ruolo centrale nel controllare la trascrizione genica. E’ stato infatti dimostrato che complessi inibitori come SWI/SNF e gli enzimi ad esso associati quali istone deacetilasi (HDAC) e protein arginin-metiltrasferasi (PRMT), siano coinvolti nel controllo della crescita, differenziazione e proliferazione cellulare. Diversi studi hanno mostrato come i meccanismi epigenetici di controllo della trascrizione genica svolgano un ruolo di primo piano nel promuovere la sopravvivenza cellulare in leucemie/linfomi di derivazione dai linfociti B come la leucemia linfatica cronica, il linfoma mantellare ed i linfomi associati al virus di Epstein-Barr (EBV). Tuttavia, molto poco e’ conosciuto circa i meccanismi epigenetici di controllo della trascrizione che divengono operativi e che contribuiscono al processo di trasformazione dei linfociti B. PRMT5 e’ un enzima che di-metila specificamente residui argininici sugli istoni (H) 3 (H3R8) ed 4 (H4R3). PRMT5 ed HDAC lavorano in concerto per reprimere la trascrizione di specifici geni oncosoppressori. In questo progetto sono stati studiati i meccanismi e le conseguenze dell’iperespressione di PRMT5 durante il processo di trasformazione dei linfociti B indotto da EBV, e’ stata dimostrata l’importanza di questo enzima nel processo di trasformazione, e sono stati studiati nuovi metodi per inibirne l’espressione/attivita’. In particolare si e’ dimostrato che l’espressione di PRMT5 e’ ridotta o assente in linfociti B normali (o attivati da stimoli fisiologici) ed elevata in linee cellulari linfoblastoidi immortalizzate o completamente trasformate. Elevati livelli citosolici di PRMT5 sono detectabili dopo 4 giorni dall’infezione di linfociti B normali con EBV, PRMT5 e’ detectabile a livello nucleare, dove esercita la sua funzione repressoria la trascrizione, a partire dal giorno 8. L’utilizzo di specifici small interference RNAs (siRNA) in linee cellulari linfoblastoidi ha permesso di dimostrare la riduzione dell’espressione di PRMT5, la riduzione della metilazione degli istoni target di PRMT5, inibizione della proliferazione cellulare e abbassamento della soglia di sensibilita’ cellulare a stimoli pro-apoptotici. Esperimenti di co-immunoprecipitazione cromatinica hanno permesso di evidenziare che in queste cellule PRMT5 e’ parte di un complesso proteico a funzione inibitoria e che questo complesso si lega alla regione promotrice di specifici geni oncosoppressori quali ST7, GAS e NM23, inibendone la trascrizione. Si e’ inoltre provveduto a sviluppare una categoria di inibitori allosterici di PRMT5: l’attivita’ terapeutica/la specificita’ in vitro e la modalita’ di somministrazione ottimale in modelli murini di linfoma non-Hodgkin, sono in corso di valutazione.
A chemiluminometric method for the determination of urea in serum using a three‐enzyme bioreactor (1988)

A flow injection chemiluminometric assay for urea has been developed based on a minicolumn bioreactor packed with immobilized enzyme-bearing glass beads. The reactor contains immobilized urease, L-glutamate dehydrogenase and L-glutamate oxidase, aligned in this order (upstream to the downstream). When the sample is introduced into the bioreactor, urea is first hydrolysed by urease to produce ammonia, which is then converted into L-glutamate by L-glutamate dehydrogenase. L-Glutamate is finally oxidized by L-glutamate oxidase to produce hydrogen peroxide, which is quantified by measuring chemiluminescence emitted upon admixing with luminol and potassium ferricyanide. One assay cycle is completed within 1 minute. The method is sensitive (detection limit 0.5 nmol) and is linear in the range 0-30 mmol/l. It can be readily applied to the determination of urea in human serum, and requires no blank corrections for ammonia and/or L-glutamate present in serum samples.
Establishing mechanisms affecting the individual response to ionizing radiation (2019)

<b>Purpose:</b> Humans are increasingly exposed to ionizing radiation (IR). Both low (<100 mGy) and high doses can cause stochastic effects, including cancer; whereas doses above 100 mGy are needed to promote tissue or cell damage. 10-15% of radiotherapy (RT) patients suffer adverse reactions, described as displaying radiosensitivity (RS). Sensitivity to IR's stochastic effects is termed radiosusceptibility (RSu). To optimize radiation protection we need to understand the range of individual variability and underlying mechanisms. We review the potential mechanisms contributing to RS/RSu focusing on RS following RT, the most tractable RS group.<b>Conclusions:</b> The IR-induced DNA damage response (DDR) has been well characterized. Patients with mutations in the DDR have been identified and display marked RS but they represent only a small percentage of the RT patients with adverse reactions. We review the impacting mechanisms and additional factors influencing RS/RSu. We discuss whether RS/RSu might be genetically determined. As a recommendation, we propose that a prospective study be established to assess RS following RT. The study should detail tumor site and encompass a well-defined grading system. Predictive assays should be independently validated. Detailed analysis of the inflammatory, stress and immune responses, mitochondrial function and life style factors should be included. Existing cohorts should also be optimally exploited.
Kernel‐based orthogonal projections to latent structures (K‐OPLS) (2007)

Abstract The orthogonal projections to latent structures (OPLS) method has been successfully applied in various chemical and biological systems for modeling and interpretation of linear relationships between a descriptor matrix and response matrix. A kernel‐based reformulation of the original OPLS algorithm is presented where the kernel Gram matrix is utilized as a replacement for the descriptor matrix. This enables usage of the ‘kernel trick’ to efficiently transform the data into a higher‐dimensional feature space where predictive and response‐orthogonal components are calculated. This strategy has the capacity to improve predictive performance considerably in situations where strong non‐linear relationships exist between descriptor and response variables while retaining the OPLS model framework. We put particular focus on describing properties of the rearranged algorithm in relation to the original OPLS algorithm. Four separate problems, two simulated and two real spectroscopic data sets, are employed to illustrate how the algorithm enables separate modeling of predictive and response‐orthogonal variation in the feature space. This separation can be highly beneficial for model interpretation purposes while providing a flexible framework for supervised regression. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Limb movement adaptations in horses with experimentally induced fore‐ or hindlimb lameness (1996)

The kinematic patterns of all limbs of 11 clinically nonlame Dutch Warmblood horses were studied during induced supporting limb lameness to gain insight into the compensation mechanisms horses use to manage lameness and to test kinematic limb variables for their significance as lameness indicators. Using the locomotion analysis system CODA-3, the kinematics of the horses were recorded while walking (1.6 m/s) and trotting (3.5 m/s) on a treadmill. A transient lameness model, evoking pressure on the hoof sole, was used to induce 3 degrees of fore- and hindlimb lameness. Joint angle patterns and hoof movements were analysed using joint angle/time diagrams and the hoof trajectories in the sagittal plane. Quantitative analysis of 13 selected variables in each limb was done using a 2-way analysis of variance. Hyperextension of the fetlock joint and flexion of the coffin joint during the stance phase decreased significantly (P < 0.05) in the lame limb, both in fore- and hindlimb lameness, at both gaits. In the contralateral nonlame limbs both variables increased compensatorily. Flexion increased with increasing lameness in the proximal joints, i.e. the shoulder joint and even more the tarsal joint of the lame limb. The retraction of both forelimbs decreased during forelimb lameness at the walk, while in the lame hindlimb the protraction decreased. The hoof arcs were lower in the lame limb than in the nonlame limb, due to an increased hoof height in the nonlame limb during forelimb lameness and to a decreased height in the lame limb during hindlimb lameness. It was concluded that patterns of the distal joints reflect the different loadings of the limbs during lameness. Proximal joints acted as load dampers to reduce peak forces in the lame limb. Hyperextension of the fetlock and flexion of the coffin joint proved to be the most sensitive indicators for fore- and hindlimb lameness.
Real-Time Robot Path Planning Based on a Modified Pulse-Coupled Neural Network Model (2009)

This paper presents a modified pulse-coupled neural network (MPCNN) model for real-time collision-free path planning of mobile robots in nonstationary environments. The proposed neural network for robots is topologically organized with only local lateral connections among neurons. It works in dynamic environments and requires no prior knowledge of target or barrier movements. The target neuron fires first, and then the firing event spreads out, through the lateral connections among the neurons, like the propagation of a wave. Obstacles have no connections to their neighbors. Each neuron records its parent, that is, the neighbor that caused it to fire. The real-time optimal path is then the sequence of parents from the robot to the target. In a static case where the barriers and targets are stationary, this paper proves that the generated wave in the network spreads outward with travel times proportional to the linking strength among neurons. Thus, the generated path is always the global shortest path from the robot to the target. In addition, each neuron in the proposed model can propagate a firing event to its neighboring neuron without any comparing computations. The proposed model is applied to generate collision-free paths for a mobile robot to solve a maze-type problem, to circumvent concave U-shaped obstacles, and to track a moving target in an environment with varying obstacles. The effectiveness and efficiency of the proposed approach is demonstrated through simulation and comparison studies.
Adoption and Effects of Software Engineering Best Practices in Machine Learning (2020)

The increasing reliance on applications with ML components calls for mature engineering techniques that ensure these are built in a robust and future-proof manner.<br> We aim to empirically determine the state of the art in how teams develop, deploy and maintain software with ML components.<br> We mined both academic and grey literature and identified 29 engineering best practices for ML applications.<br> We conducted a survey among \finalFiltered~practitioners to determine the degree of adoption for these practices and to validate their perceived effects.<br> Using the survey responses, we quantified practice adoption, differentiated along demographic characteristics, such as geography or team size. Our findings indicate, for example, that larger teams tend to adopt more practices, and that traditional software engineering practices tend to have lower adoption than \ac{ML} specific practices.<br> Also, the statistical models can accurately predict perceived effects such as agility, software quality and traceability, from the degree of adoption for specific sets of practices.<br> Combining practice adoption rates with practice importance, as revealed by statistical models, we identify practices that are important but have low adoption and practices that are widely adopted but are less important for the effects we studied.<br> <br> Overall, our survey and response analysis provide a quantitative basis for <br> assessment and step-wise improvement of practice adoption by ML teams.
Atherosclerotic disease and management challenges with nanomedicine: EU FP7 NMP funded “NanoAthero” and “CosmoPHOS-nano” large-scale projects (2014)

Abstract Atherosclerosis is the most important arterial wall disease that causes arterial stenosis and may lead to the clinical manifestations of angina, heart attack and stroke. There is a demanding unmet medical need for new approaches for early diagnosis and improved/novel targeted therapies and therapy monitoring of atherosclerosis. This is the focus of two European large scale projects, the NanoAthero and the CosmoPHOS-nano by using nanomedicine. The aim is to demonstrate that nanotechnology-enabled systems can be successfully developed and clinically proven to be safe and effective in tackling cardiovascular diseases.
Detrimental consequences after intimal disruption of subclavian artery during transcathether aortic valve implantation (2023)

Though TAVI is a well-advanced technique complications are not completely avertable. It is thus advisable to have patients discussed in the heart team encompassing all potentially involved specialties.
A Kraft-Type Sufficient Condition for the Existence of $D$-Ary Fix-Free Codes (2010)

A greedy scheme called Greedy Codeword Assignment Scheme (GCAS) is proposed to assign D-ary codewords to the given code-lengths ¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ,¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ,...,¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> , so that they satisfy the fix-free property. This scheme guarantees that a D-ary fix-free code can be obtained whenever ¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i=1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-¿</sup> ¿ ¿(D), where ¿(D) is equal to 5/8 for D even and very close to 5/8 for D odd. This result can be regarded as an extension of Yekhanin's theorem on the existence of binary fix-free codes. In the special case D=2 , the greediness of GCAS enables us to prove that if mini ¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> = 2, the inequality ¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i=1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-¿</sup> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sup> ¿ 21/32 implies the existence of a binary fix-free code with code-lengths ¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ,¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ,...,¿ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> .
Purine Metabolism in Toxoplasma gondii (1989)

We have studied the incorporation and interconversion of purines into nucleotides by freshly isolated Toxoplasma gondii. They did not synthesize nucleotides from formate, glycine, or serine. The purine bases hypoxanthine, xanthine, guanine, and adenine were incorporated at 9.2, 6.2, 5.1, and 4.3 pmol/10(7) cells/h, respectively. The purine nucleosides adenosine, inosine, guanosine, and xanthosine were incorporated at 110, 9.0, 2.7, and 0.3 pmol/10(7) cells/h, respectively. Guanine, xanthine, and their respective nucleosides labeled only guanine nucleotides. Inosine, hypoxanthine, and adenine labeled both adenine and guanine nucleotide pools at nearly equal ratios. Adenosine kinase was greater than 10-fold more active than the next most active enzyme in vitro. This is consistent with the metabolic data in vivo. No other nucleoside kinase or phosphotransferase activities were found. Phosphorylase activities were detected for guanosine and inosine; no other cleavage activities were detected. Deaminases were found for adenine and guanine. Phosphoribosyltransferase activities were detected for all four purine nucleobases. Interconversion occurs only in the direction of adenine to guanine nucleotides.
Optimization of spot-size converter for low polarization dependent loss of waveguide photodetector (2013)

We present an optimization of spot-size converter (SSC) of waveguide photodetector (PD) for small polarization dependent loss (PDL). Beam-propagation method simulation gives responsivity for each polarization and SSC structure. From the calculated responsivity data, optimum structure of SSC is determined that can be implemented with a sufficient process tolerance. We confirm the optimization by measuring PDL of waveguide PD designed according to the structure obtained through the simulation.
ChemInform Abstract: Preparation of Functionalized Aryl(diallyl)ethoxysilanes and Their Palladium‐Catalyzed Coupling Reactions Giving Sol—Gel Precursors. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Slug, a Cancer‐Related Transcription Factor, is Involved in Vascular Smooth Muscle Cell Transdifferentiation Induced by Platelet‐Derived Growth Factor‐BB During Atherosclerosis (2020)

Background Heart attacks and stroke often result from occlusive thrombi following the rupture of vulnerable atherosclerotic plaques. Vascular smooth muscle cells (VSMCs) play a pivotal role in plaque vulnerability because of their switch towards a proinflammatory/macrophage-like phenotype when in the context of atherosclerosis. The prometastatic transcription factor Slug/Snail2 is a critical regulator of cell phenotypic transition. Here, we aimed to investigate the role of Slug in the transdifferentiation process of VSMCs occurring during atherogenesis. Methods and Results In rat and human primary aortic smooth muscle cells, Slug protein expression is strongly and rapidly increased by platelet-derived growth factor-BB (PDGF-BB). PDGF-BB increases Slug protein without affecting mRNA levels indicating that this growth factor stabilizes Slug protein. Immunocytochemistry and subcellular fractionation experiments reveal that PDGF-BB triggers a rapid accumulation of Slug in VSMC nuclei. Using pharmacological tools, we show that the PDGF-BB-dependent mechanism of Slug stabilization in VSMCs involves the extracellular signal-regulated kinase 1/2 pathway. Immunohistochemistry experiments on type V and type VI atherosclerotic lesions of human carotids show smooth muscle-specific myosin heavy chain-/Slug-positive cells surrounding the prothrombotic lipid core. In VSMCs, Slug siRNAs inhibit prostaglandin E2 secretion and prevent the inhibition of cholesterol efflux gene expression mediated by PDGF-BB, known to be involved in plaque vulnerability and/or thrombogenicity. Conclusions Our results highlight, for the first time, a role of Slug in aortic smooth muscle cell transdifferentiation and enable us to consider Slug as an actor playing a role in the atherosclerotic plaque progression towards a life-threatening phenotype. This also argues for common features between acute cardiovascular events and cancer.
A biomedical events extracted approach based on phrase structure tree (2017)

Biomedical events, known as fine-grained and complex relations, are very important to biomedical information extraction. Automatically extracting biomedical events from the literature has attracted significant interest in recent years. Biomedical Event Extraction (BEE) is a difficult and urgent problem in biomedical information extraction area due to the unstructured text and its lexical variations. This paper presents a BEE approach based on phrase structure tree consisting of text preprocessing, syntax parsing and event trigger recognition for the extracting the biomedical events. The experimental results show that our method performs well. Event extraction results are comparable to the state of the art system. We develop the biomedical event extraction system, which can be accessed by http://210.28.186.168:8080/bioEvent/.
<title>Fast stable thermal fiber switch in a Sagnac interferometer</title> (1998)

We demonstrate a fast, stable, all-optical switch using a thermal effect in cobalt-doped fiber. 46 ns switching is accomplished in a 10-m Sagnac loop containing a 2.55-cm length of doped fiber. Compared to other demonstrated all- optical switches using doped fibers, this switch offers a significant increase in speed and stability, as well as a significant reduction in fiber length.
Effect of Varying Live Weight and Preslaughter Fast Period on the Slaughter, Storage, Cutting and Cooking Losses of Lambs2 (1966)

Eighty-six lambs were slaughtered at 33, 40,50 or 60 kg. preshrunk, shorn live weight after being fasted for 24 or 72 hr. Marketing losses were determined to include preslaughter, slaughter, cooler and cutting losses. Cooking losses were then determined on representative loin chops from each lamb. Although body weight significantly affected all marketing losses measured, these were often offsetting effects, and the percent of the original lamb, ranging from 32.7 to 34.6, included in the four trimmed retail cuts (leg, loin, rack and shoulder) was not greatly affected by body weight in the lambs fasted for 24 hr. The range was greater (30.7 to 34.1%) in the lambs fasted 72 hr., as a reduction due to fasting was noted in the lightest lambs. The chemical composition of the wholesale rack and retail loin chops was affected by body weight. Cuts from the larger lambs were higher in ether extract and lower in water, protein and ash content. Cooking tended to diminish these differences. No differences due to preslaughter shrink period were noted on cooking losses.
Secretion Expression and Activity Assay of a Novel Fusion Protein of Thrombopoietin and Interleukin-6 in Pichia pastoris (2007)

Thrombopoietin (TPO) is an important haematopoietic factor in megakaryocytic activities as well as in platelet production. Interleukin 6 (IL-6) can co-stimulate TPO-dependent formation of colony forming unit of megakaryocyte (CFU-Meg) growth which could be responsible for residual platelet formation in TPO-deficient or c-mpl-deficient animals. In this report, we demonstrated the development of a high-level expression system to produce a 78-kDa human fusion protein IL-6/TPO (named ZH646). This was achieved by constructing the expression vector pPICZalpha-A-IL-6-linker-TPO, and obtained the recombinant yeast GS115, which then efficiently secreted into a medium with a yield of 30 mg/l from the supernatant of the yeast culture in flask. ZH646 was then purified using two steps via DEAE-Sephacel chromatography and Mono Q columns. Activity assay showed that ZH646 could significantly stimulate the formation of CFU-Meg and the proliferation of Dami cells in vitro in a dose-dependent manner. In addition, ZH646 also showed thrombopoietic effect in normal mice, and the ability to enhance recovery of normal platelet counts after myelosuppression mice. These results suggested that ZH646 is a novel protein, and its activities are much stronger than that of TPO or IL-6 alone. ZH646 therefore has a broad spectrum of megakaryopoiesis activity associated with platelet production.