gebhart/patrepeval huggingface dataset:
Biogenic amines and drug research (1984)

From time to time during the course of basic biochemical and pharmacological research, discoveries are made which reveal the order and elegance of what seems to be the bewildering array of molecules responsible for the life of even the simplest cell. The isolation of deoxyribonucleic acid (DNA) in 1869 and the elucidation of its composition and structure more than 80 years later, for example, revealed not only that this molecule was to be found in the cells of every living thing from bacteria to man but also that the genetic code is uniform throughout life. This led to a tremendous breakthrough in cellular biology, and present-day concepts of protein synthesis and cancer chemotherapy, among others, are rooted in our understanding of DNA.
Regulation of gene expression by protein lysine acetylation in Salmonella (2020)

Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNA-binding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.
Diagnoses and treatment proposals in periodontal treatment. A comparison between dentists, dental hygienists and undergraduate students. (2015)

The aim of this study is to find out how professionals in Swedish dental care perform diagnostic procedures in general. Is there a common ground between dentists and dental hygienists concerning sharing different job assignments in an effective way? Are the methods of treatment used in accordance with degree of severity of the disease and to what extent is proposed treatment in accordance with the National Guidelines? A questionnaire consisting of three different patient cases with periodontal disease was sent to 804 private practitioners, 809 dentists in Dental Public Service, 802 dental hygienists and 40 dental students on their final semester at the Dental School in Malmö. The questionnaire was completed by 1,103 respondents (47%). A majority of all practitioner groups (94%) found that a relatively healthy patient had disease, the risk for developing further disease was deemed none too low by 97%, but 91% wanted to give preventive care. A vast majority suggested more dental care to healthy patients as compared to patients with severe periodontal disease. In Conclusion the two groups, i.e. dentists and dental hygienists, did not to a sufficiently high degree share views on diagnosis and treatment, in order to optimize the resources in dentistry. The delivery of dental care was not in line with the severity of disease and too much attention was paid to the needs of relatively healthy persons. To change this pattern, the incentives in and structure of the national assurance system could be adapted. Furthermore, the knowledge basis for periodontal diagnosis and treatment needs, with special reference to the National Guidelines, should to a higher degree be shared by all caregivers.
Submerged culture conidial germination and conidiation of the bioherbicideColletotrichum truncatum are influenced by the amino acid composition of the medium (1993)

Submerged culture experiments were conducted to determine the optimal nitrogen source for rapidly producing conidia of the bioherbicide,Colletotrichum truncatum. Germination ofC. truncatum conidial inocula in submerged culture occurred most rapidly (>95% in 6 h) in media provided with a complete complement of amino acids. When (NH4)2SO4, urea, or individual amino acids were provided as the sole nitrogen source, conidial germination was less than 20% after 6 h incubation. Conidia production was delayed inC. truncatum cultures grown in media with urea or individual amino acids as nitrogen sources compared to cultures supplied with Casamino acids or complete synthetic amino acid nitrogen sources. The use of methionine, lysine, tryptophan, isoleucine, leucine or cysteine as a sole nitrogen source severely inhibitedC. truncatum conidia production. Media with synthetic amino acid mixtures less these inhibitory amino acids produced significantly higher conidia yields compared to media with amino acid mixtures containing these amino acids. When various amounts of each individual inhibitory amino acid were added to media which contained amino acid mixtures, cysteine and methionine were shown to be most effective in reducing conidiation. An optimal nitrogen source forC. truncatum conidiation in submerged culture should contain a complete mixture of amino acids with low levels of cysteine, methionine, leucine, isoleucine, lysine and tryptophan for rapid conidiation and optimal conidia yield.
Labelling of olfactory ensheathing cells with micron‐sized particles of iron oxide and detection by MRI (2012)

A crucial issue in transplant-mediated repair of the damaged central nervous system (CNS) is serial non-invasive imaging of the transplanted cells, which has led to interest in the application of magnetic resonance imaging (MRI) combined with designated intracellular magnetic labels for cell tracking. Micron-sized particles of iron oxide (MPIO) have been successfully used to track cells by MRI, yet there is relatively little known about either their suitability for efficient labelling of specific cell types, or their effects on cell viability. The purpose of this study was to develop a suitable MPIO labelling protocol for olfactory ensheathing cells (OECs), a type of glia used to promote the regeneration of CNS axons after transplantation into the injured CNS. Here, we demonstrate an OEC labelling efficiency of >90% with an MPIO incubation time as short as 6 h, enabling intracellular particle uptake for single-cell detection by MRI without affecting cell proliferation, migration and viability. Moreover, MPIO are resolvable in OECs transplanted into the vitreous body of adult rat eyes, providing the first detailed protocol for efficient and safe MPIO labelling of OECs for non-invasive MRI tracking of transplanted OECs in real time for use in studies of CNS repair and axon regeneration.
Sandcrust (2017)

System-level development has been dominated by traditional programming languages such as C and C++ for decades. These languages are inherently unsafe regarding memory management. Even experienced developers make mistakes that open up security holes or compromise the safety properties of software. The Rust programming language is targeted at the systems domain and aims to eliminate memory-related programming errors by enforcing a strict memory model at the language and compiler level. Unfortunately, these compile-time guarantees no longer hold when a Rust program is linked against a library written in unsafe C, which is commonly required for functionality where an implementation in Rust is not yet available.
Clinical Presentation of Inhalational Anthrax Following Bioterrorism Exposure (2001)

The use of anthrax as a weapon of biological terrorism has moved from theory to reality in recent weeks. Following processing of a letter containing anthrax spores that had been mailed to a US senator, 5 cases of inhalational anthrax have occurred among postal workers employed at a major postal facility in Washington, DC. This report details the clinical presentation, diagnostic workup, and initial therapy of 2 of these patients. The clinical course is in some ways different from what has been described as the classic pattern for inhalational anthrax. One patient developed low-grade fever, chills, cough, and malaise 3 days prior to admission, and then progressive dyspnea and cough productive of blood-tinged sputum on the day of admission. The other patient developed progressively worsening headache of 3 days' duration, along with nausea, chills, and night sweats, but no respiratory symptoms, on the day of admission. Both patients had abnormal findings on chest radiographs. Non-contrast-enhanced computed tomography of the chest showing mediastinal adenopathy led to a presumptive diagnosis of inhalational anthrax in both cases. The diagnoses were confirmed by blood cultures and polymerase chain reaction testing. Treatment with antibiotics, including intravenous ciprofloxacin, rifampin, and clindamycin, and supportive therapy appears to have slowed the progression of inhalational anthrax and has resulted to date in survival.
Optically-controlled optical gate using a double diode structure (2003)

A new device concept enabling ultra-short optically controlled optical gating is demonstrated. Using a dual-diode GaAs multiple-quantum well (MQW) structure, low power surface-normal switching times of /spl sim/10 ps are achieved in this proof-of-principle device.
Separation of the influence of in-plane displacement in multiaperture speckle shear interferometry (1994)

An imaging system with its aperture fully open or with a multiaperture mask in front has been used for carrying out speckle shear interferometry. The shearing is achieved by installing shear elements in front of the imaging system. The multiaperture configuration has built-in in-plane displacement sensitivity, and hence shear fringes obtained from multiaperture shear interferometer always carry the in-plane displacement contribution. This problem does not arise when the full aperture of the lens is used. A three-aperture speckle shear interferometric technique is introduced here to separate the in-plane displacement and slope contributions from the shear interferogram. Detailed theoretical and experimental results are presented.
A projective drawing system (2001)

Article Share on A projective drawing system Authors: Osama Tolba Massachusetts Institute of Technology, Cambridge Massachusetts Institute of Technology, CambridgeView Profile , Julie Dorsey Massachusetts Institute of Technology, Cambridge Massachusetts Institute of Technology, CambridgeView Profile , Leonard McMillan Massachusetts Institute of Technology, Cambridge.0 Massachusetts Institute of Technology, Cambridge.0View Profile Authors Info & Claims I3D '01: Proceedings of the 2001 symposium on Interactive 3D graphicsMarch 2001 Pages 25–34https://doi.org/10.1145/364338.364342Online:01 March 2001Publication History 34citation1,154DownloadsMetricsTotal Citations34Total Downloads1,154Last 12 Months14Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Flavopiridol Induces Mitochondrial-Mediated Apoptosis in Murine Glioma GL261 Cells via Release of Cytochrome c and Apoptosis Inducing Factor (2003)

Glioblastoma (GBM) remains one of the most challenging solid cancers to treat due to its highly proliferative, angiogenic and invasive nature. The small molecule CDK inhibitor, flavopiridol, has demonstrated antitumor activity in human xenograft models and is currently in clinical trials showing efficacy in patients with advanced disease. We have developed an experimental animal model using the murine glioma GL261 cells as a novel in vivo system to screen potential therapeutic agents for GBM. Results of in vitro testing demonstrate that flavopiridol has several relevant clinical characteristics such as its ability to: 1. inhibit cell growth; 2. inhibit cell migration; 3. decrease expression of cyclin D1, CDK4 and p21; 4. induce apoptosis in cells with high levels of p27 expression; and 5. decrease the expression of the anti-apoptotic protein Bcl-2. The mechanism by which flavopiridol induces apoptosis is mitochondrial-mediated. We demonstrate by electron microscopy and immunohistochemistry that drug treatment induces mitochondrial damage that was accompanied by the release of cytochrome c into the cytosol together with the translocation of apoptosis inducing factor (AIF) into the nucleus. This finding in murine glioma cells differs from the mechanism of flavopiridolinduced cell death reported by us for human glioma cells (Alonso et al., Mol Cancer Ther 2003; 2:139) where drug treatment induced a caspase- and cytochrome c-independent pathway in the absence of detectable damage to mitochondria. In apoptotic human glioma cells only translocation of AIF into the nucleus occurred. Thus, the same drug kills different types of glioma cells by different mitochondrial-dependent pathways.
Investigation of permanent magnets in low-cost position tracking (2016)

<i>PURPOSE</i>: Low cost portable ultrasound systems could see improved utility if similarly low cost portable trackers were developed. Permanent magnet based tracking systems potentially offer adequate tracking accuracy in a small workspace suitable for ultrasound image reconstruction. In this study the use of simple permanent magnet tracking techniques is investigated to determine feasibility for use in an ultrasound tracking system. <i>METHODS</i>: Permanent magnet tracking requires finding a position input into a field model which minimizes the error between the measured field, and the field expected from the model. A simulator was developed in MATLAB to determine the effect of sources of error in permanent magnet tracking systems. Insights from the simulations were used to develop a calibration and tracking experiment to determine the accuracy of a simple and low cost permanent magnet tracking system. <i>RESULTS</i>: Simulation and experimental results show permanent magnet based tracking to be highly sensitive to errors in sensor measurements, calibration and experimental setup. The reduction in field strength of permanent magnets lowers with the cube of distance, which leads to very poor signal-to-noise ratios at distances above 20 cm. Small errors in experimental setup also led to high tracking error. <i>CONCLUSION</i>: Permanent magnet tracking was found to be less accurate than is clinically useful, and highly sensitive to errors in sensors and experimental setup. Sensor and calibration limitations make simple permanent magnet tracking systems a poor choice given the present state of sensor technology.
Schutzgruppengesteuerte Oberflächenchemie – Organisation und temperaturinduzierte Kupplung von 4,4′‐Di(tert‐Butoxycarbonylamino)biphenyl auf Metalloberflächen (2009)

Abstract Wie die Perlen einer Kette wurden molekulare Bausteine auf einer Oberfläche vororganisiert, um sie anschließend miteinander zu verbinden. Dabei wurde sowohl die supramolekulare Anordnung der Reaktanten als auch die anschließende thermische Aktivierung zur Verknüpfung von der Schutzgruppe bestimmt. magnified image
An Efficient Technique for Large Mini-batch Challenge of DNNs Training on Large Scale Cluster (2020)

Distributed deep learning using large mini-batches is a key strategy to perform the deep learning as fast as possible, but it represents a great challenge as it is difficult to achieve high scaling efficiency when using large clusters without compromising accuracy. The particular problem in this challenge is decreasing the number of model update iterations in whole of training. Thus, we need a technique which can converge the validation accuracy with a small number of iterations to address this challenge. In this paper, we introduce a novel technique, Final Polishing. This technique adjusts the means and variances in the batch normalization and mitigates the difference of normalization between validation datasets and augmented training datasets. By applying the technique, we achieved top-1 validation accuracy of 75.08% with mini-batch size of 81,920, with 2,048 GPUs and completed the training of ResNet-50 in 74.7 seconds.In addition, targeting top-1 validation accuracy of 75.9% or more, we tried additional parameters tuning. Then, we adjusted the number of GPUs and hyperparameters of DNNs with Final Polishing, and we also achieved top-1 validation accuracy of 75.97% with mini-batch size of 86,016, with 3,072 GPUs and completed the training of ResNet-50 in 62.1 seconds.
Parallel optimization of large join queries with set operators and aggregates in a parallel environment supporting pipeline (1996)

Proposes a parallel optimizer for queries containing a large number of joins, as well as set operators and aggregate functions. The platform for the execution is a shared-disk multiprocessor machine supporting bushy parallelism and pipeline processing. Our model partitions the query into almost independent subtrees that can be optimized simultaneously, and it applies an enhanced variation of the iterative improvement technique on those subtrees which contain a large number of joins; this technique is parallelized, too. In order to estimate the cost of the states constructed during the optimization of join subtrees, cost formulae are developed that estimate the cost of relational algebra operators when executed across coalescing pipes.
Disturbance-Aware Neuro-Optimal System Control Using Generative Adversarial Control Networks (2020)

Disturbance, which is generally unknown to the controller, is unavoidable in real-world systems and it may affect the expected system state and output. Existing control methods, like robust model predictive control, can produce robust solutions to maintain the system stability. However, these robust methods trade the solution optimality for stability. In this article, a method called generative adversarial control networks (GACNs) is proposed to train a controller via demonstrations of the optimal controller. By formulating the optimal control problem in the presence of disturbance, the controller trained by GACNs obtains neuro-optimal solutions without knowing the future disturbance and determines the objective function explicitly. A joint loss, composed of the adversarial loss and the least square loss, is designed to be used in the training of the generator. Experimental results on simulated systems with disturbance show that GACNs outperform other compared control methods.
Abstract 649: Endothelial-derived Sphingolipids Preserve Systemic Vascular Function And Blood Pressure (2014)

Endothelial dysfunction is a critical event in many cardiovascular diseases including hypertension. Although lipid signaling is implicated in endothelial dysfunction and cardiovascular diseases, specific molecular mechanisms are poorly understood. Here we report a novel regulation of endothelial sphingolipid synthesis by Nogo-B, membrane protein of the endoplasmic reticulum that modulates local sphingolipid production with direct effects on vascular function and blood pressure. Nogo-B inhibits serine palmitoyltransferase, rate-limiting enzyme of the sphingolipid de novo synthesis, controlling endothelial sphingosine 1-phosphate production and its autocrine G-protein-coupled receptor-dependent signaling actions. Mice lacking Nogo-B are hypotensive (90.1±1.6 vs. 119.9±2.6 mmHg WT mice), resistant to Ang-II (500ng/Kg/min)-induced hypertension (150.4±2.5 vs. 108.4±1.5 mmHg, compared to WT mice, 24 days after AngII infusion), and preserve endothelial function and nitric oxide release. Pharmacological inhibition of serine palmitoyltransferase with myriocin in mice that lack Nogo-B reinstated endothelial dysfunction and Ang-II-induced hypertension (143.9±1.5 vs. 90.1±1.6 mmHg, myriocin vs. vehicle treated Nogo-A/B-/- mice). Our study identifies Nogo-B as a key inhibitor of local sphingolipid synthesis and indicates that autocrine sphingolipids signaling within the endothelium are critical for vascular function and blood pressure homeostasis.
Microscopic calculation of the optical properties and intrinsic losses in the methylammonium lead iodide perovskite system (2018)

For opto-electronic and photo-voltaic applications of perovskites, it is essential to know the optical properties and intrinsic losses of the used materials. A systematic microscopic analysis is presented for the example of methylammonium lead iodide where density functional theory is used to calculate the electronic band structure as well as the dipole and Coulomb matrix elements. These results serve as input for a many-body quantum approach used to compute the absorption, photoluminescence, and the optical and Auger losses for a wide range of application conditions. To illustrate the theory, the excitonic properties of the material system are investigated and numerical results are presented for typical photo-voltaic operation conditions and for the elevated carrier densities needed for laser operation.
The Influence of Oral Contraceptives on the Time-Integral of Thrombin Generation (Thrombin Potential) (1993)

The thrombin potential (TP) has been defined as the time integral of (i.e. the area under) the thrombin generation curve. It has been shown that this parameter decreases with all types of anticoagulant treatment and increases with ATIII deficiency. We evaluated the use of this parameter for detection of the hypercoagulative state known to accompany oral contraception. In fresh frozen control plasma the TP could be determined with high reproducibility (n = 82, c.v. 2.9%). The TP was linearly diminished by mixing fresh frozen plasma with prothrombin deficient plasma while a high coefficient of correlation was observed (r = 0.997). Women using oral contraceptives showed a significantly (p < 0.0001) higher TP (TP = 569 nM.min, SD = 55, n = 17), compared to men or, to women not using oral contraceptives (TP = 484 nM.min, SD = 52, n = 41). This suggests that the thrombin potential indicates the prethrombotic state known to exist in women using oral contraceptives.