gebhart/patrepeval huggingface dataset:
The SpoIIE phosphatase, the sporulation septum and the establishment of forespore‐specific transcription in Bacillus subtilis: a reassessment (1999)

Making a spore in Bacillus subtilis requires the formation of two cells, the forespore and the mother cell, which follow dissimilar patterns of gene expression. Cell specificity is first established in the forespore under the control of the sigma F factor, which is itself activated through the action of the SpoIIE serine phosphatase, an enzyme targeted to the septum between the two cells. Deletion of the 10 transmembrane segments of the SpoIIE protein leads to random distribution of SpoIIE in the cytoplasm. Activation of sigma F is slightly delayed and less efficient than in wild type, but it remains restricted to the forespore in a large proportion of cells and the bacteria sporulate with 30% efficiency. Overexpression of the complete SpoIIE protein in a divIC mutant leads to significant sigma F activity, indicating that the septum requirement for activating sigma F can be bypassed. In contradiction to current models, we propose that genetic asymmetry is not created by unequal distribution of SpoIIE within the sporangium, but by exclusion of an inhibitor of SpoIIE from the forespore. This putative inhibitor would be a cytoplasmic molecule that interacts with SpoIIE and shuts off its phosphatase activity until it disappears specifically from the forespore.
Computer vision algorithms and hardware implementations: A survey (2019)

The field of computer vision is experiencing a great-leap-forward development today. This paper aims at providing a comprehensive survey of the recent progress on computer vision algorithms and their corresponding hardware implementations. In particular, the prominent achievements in computer vision tasks such as image classification, object detection and image segmentation brought by deep learning techniques are highlighted. On the other hand, review of techniques for implementing and optimizing deep-learning-based computer vision algorithms on GPU, FPGA and other new generations of hardware accelerators are presented to facilitate real-time and/or energy-efficient operations. Finally, several promising directions for future research are presented to motivate further development in the field.
Deep Learning for Unsupervised Insider Threat Detection in Structured Cybersecurity Data Streams (2017)

Analysis of an organization's computer network activity is a key component of early detection and mitigation of insider threat, a growing concern for many organizations. Raw system logs are a prototypical example of streaming data that can quickly scale beyond the cognitive power of a human analyst. As a prospective filter for the human analyst, we present an online unsupervised deep learning approach to detect anomalous network activity from system logs in real time. Our models decompose anomaly scores into the contributions of individual user behavior features for increased interpretability to aid analysts reviewing potential cases of insider threat. Using the CERT Insider Threat Dataset v6.2 and threat detection recall as our performance metric, our novel deep and recurrent neural network models outperform Principal Component Analysis, Support Vector Machine and Isolation Forest based anomaly detection baselines. For our best model, the events labeled as insider threat activity in our dataset had an average anomaly score in the 95.53 percentile, demonstrating our approach's potential to greatly reduce analyst workloads.
Pathogenic Potential of Myeloblastosis-Associated Virus: Implication of ENV Proteins for Osteopetrosis Induction (1993)

To identify the nucleotide sequences responsible for the tumorigenic specificity of myeloblastosis-associated virus (MAV) we have established the complete nucleotide sequences of three infectious clones inducing either both osteopetrosis and nephroblastoma [MAV2(O)/2 and MAV2(O)p9] or only nephroblastoma [MAV1(N)], and compared their biological properties in the same chicken host strain. The MAV2(O)p9 originally described as a type 2 strain was found to carry a hybrid env gene containing sequences of both the types 1 and 2, and it induced milder and less rapid osteopetrosis than the original MAV2(O) clone when injected into Brown Leghorn chickens. These results, together with sequence comparisons between the MAV strains examined, suggest that subtle changes in the primary structure of the TM env protein's extracellular domain are likely to affect the tumorigenic potential of MAV.
Serum antibodies to outer membrane proteins (OMPs) of Moraxella (Branhamella) catarrhalis in patients with bronchiectasis: identification of OMP B1 as an important antigen (1995)

Moraxella (Branhamella) catarrhalis is a common cause of lower respiratory tract infections in adults and of otitis media in children. Little is known about the human immune response to this bacterium. In this study, immunoblot assays were performed to detect serum immunoglobulin G antibodies directed at purified outer membrane of M. catarrhalis. Twelve serum samples, two each from six patients with bronchiectasis who were persistently colonized with this organism, were tested with their homologous M. catarrhalis sputum isolates. In all the sera, the most prominent and consistent antibody response was to a minor 84-kDa outer membrane protein, OMP B1. Immunoblot adsorption assays show that these antibodies recognize surface exposed epitopes on OMP B1. Further analysis of human serum antibodies eluted from the surface of intact bacterial cells shows that these surface-exposed epitopes on OMP B1 are heterogeneous among strains of M. catarrhalis. OMP B1 is therefore an important OMP antigen on the surface of M. catarrhalis for the human immune response to infection by this bacterium.
Stereoselectivity in fragmentation and rearrangement of α-hydroxyimino-phosphinates and -phosphonates. A synthetic approach to acylphosphon- and phosphor-amidates. Crystal structures of methyl (E)-α-hydroxyimino-benzylphenylphosphinate and methyl benzoylphenylphosphonamidate (1990)

Reaction of methyl benzoylphenylphosphinate 1 with hydroxylamine gave methyl α-hydroxy-iminobenzylphenylphosphinate 2 as a mixture of E and Z isomers with the E isomer predominating. Pure (E)-2 when heated gave methyl N-benzoylphenylphosphonamidate 3 as the sole product. In contrast, (Z)-2 when heated gave, as a result of fragmentation, mainly methyl hydrogen phenylphosphonate 4 and benzonitrile, together with methyl N-phenylcarbamoylphenylphosphinate 5 as the minor product; the latter results from Beckmann rearrangement of (Z)-2. Analogous behaviour is exhibited by the two geometrical isomers of dimethyl α-hydroxyiminobenzylphosphonate 8. The crystal structures of methyl (E)-α-hydroxyiminobenzylphenylphosphinate (E)-2 and methyl benzoylphenylphosphonamidate 3 are reported.
Pteridines, XXXVIII. Synthese und Eigenschaften von 2.4‐Diamino‐6‐ und ‐7‐oxo‐dihydropteridinen (1970)

Abstract Verschieden substituierte 2.4‐Diamino‐7‐ und ‐6‐oxo‐dihydropteridine ( 7–10 bzw. 12 –14 ) werden aus Tetraaminopyrimidinen ( 1–4 ) dargestellt und die Strukturen anhand von pK‐Werten und UV‐Spektren diskutiert.
Dynamic thermal management for high-performance microprocessors (2002)

With the increasing clock rate and transistor count of today's microprocessors, power dissipation is becoming a critical component of system design complexity. Thermal and power-delivery issues are becoming especially critical for high-performance computing systems. In this work, we investigate dynamic thermal management as a technique to control CPU power dissipation. With the increasing usage of clock gating techniques, the average power dissipation typically seen by common applications is becoming much less than the chip's rated maximum power dissipation. However system designers still must design thermal heat sinks to withstand the worse-case scenario. We define and investigate the major components of any dynamic thermal management scheme. Specifically we explore the tradeoffs between several mechanisms for responding to periods of thermal trauma and we consider the effects of hardware and software implementations. With approximate dynamic thermal management, the CPU can be designed for a much lower maximum power rating, with minimal performance impact for typical applications.
SPARSE: A Hybrid System to Detect Malcode-Bearing Documents (2008)

Embedding malcode within documents provides a convenient means of penetrating systems which may be unreachable by network-level service attacks. Such attacks can be very targeted and difficult to detect compared to the typical network worm threat due to the multitude of document-exchange vectors. Detecting malcode embedded in a document is difficult owing to the complexity of modern document formats that provide ample opportunity to embed code in a myriad of ways. We focus on Microsoft Word documents as malcode carriers as a case study in this paper. We introduce a hybrid system that integrates static and dynamic techniques to detect the presence and location of malware embedded in documents. The system is designed to automatically update its detection models to improve accuracy over time. The overall hybrid detection system with a learning feedback loop is demonstrated to achieve a 99.27% detection rate and 3.16% false positive rate on a corpus of 6228 Word documents.
Algorithm comparison for high impedance fault detection based on staged fault test (1988)

Four high-impedance fault-detection algorithms-proportional relaying, ratio ground relaying, second-order harmonic current relaying, and third-order harmonic current relaying-were simulated by mathematical models. Relaying performances using staged fault data were then compared. Results of the fault data processing were used to distinguish the detection characteristics: fault identification, stability, threshold setting adaptability, transient recovery characteristic, and availability. The operations of a ground overcurrent relay and a ratio ground relay were also checked in the test. The results can be used as a reference for the development of a reliable high-impedance fault detector.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Protein Interaction Network of Extracellular Vesicles Derived from Human Colorectal Cancer Cells (2011)

Various mammalian cells including tumor cells secrete extracellular vesicles (EVs), otherwise known as exosomes and microvesicles. EVs are nanosized bilayered proteolipids and play multiple roles in intercellular communication. Although many vesicular proteins have been identified, their functional interrelationships and the mechanisms of EV biogenesis remain unknown. By interrogating proteomic data using systems approaches, we have created a protein interaction network of human colorectal cancer cell-derived EVs which comprises 1491 interactions between 957 vesicular proteins. We discovered that EVs have well-connected clusters with several hub proteins similar to other subcellular networks. We also experimentally validated that direct protein interactions between cellular proteins may be involved in protein sorting during EV formation. Moreover, physically and functionally interconnected protein complexes form functional modules involved in EV biogenesis and functions. Specifically, we discovered that SRC signaling plays a major role in EV biogenesis, and confirmed that inhibition of SRC kinase decreased the intracellular biogenesis and cell surface release of EVs. Our study provides global insights into the cargo-sorting, biogenesis, and pathophysiological roles of these complex extracellular organelles.
Detection system of motor epileptic seizures through motion analysis with 3D accelerometers (2009)

A system of epilepsy seizure detection in real life conditions and based on inertial sensors is presented in this paper with a focus on the signal processing to recognize seizure moves. This system is based on several models of signals, one corresponding to general movements, and two others describing seizures moves. The detection algorithm evaluates for a given time window which model fits the best with the observed signals and trigger an alarm if this model is a seizure model. The signal processing algorithm is based on hidden Markov models.
TGF-β1 induces human alveolar epithelial to mesenchymal cell transition (EMT) (2005)

Our study shows that TGF-beta1 induces A549 alveolar epithelial cells to undergo EMT via Smad2 activation. Our data support the concept of EMT in lung epithelial cells, and suggest the need for further studies to investigate the phenomenon.
Nigeria - Lagos Urban Transport Project : environmental assessment (2002)

In this environmental assessment for the Lagos Urban Transport Project, which rehabilitates roads, there are a number of potential negative impacts that arise. These effects, together with measures to mitigate them, are described in this summary. Increased air pollution from exhaust emissions of equipment and machinery will be alleviated by locating equipment remotely from receptors where possible; adhering to engine maintenance schedules and standards; and including air pollution control equipment on the asphalt plant. Dust suppression equipment such as water sprays will suppress dust. Adhering to engine maintenance schedules and standards, installing and maintaining effective silencers, and timing activities will offset increased noise levels at residential properties, schools, businesses, and places of worship. Effective site management controls will reduce flood damage to property. Sensitive siting of heavy equipment and materials storage will avoid reducing activity for local traders. Planning maintenance works and implementing traffic management measures which minimize disruption to traffic flows will control the increase in journey times. Safe and clearly signed alternative routes will reduce the increased risk to pedestrians through restrictions to access routes. Suitable traffic control measures will be implemented to avoid road traffic accidents.
Ex vivo gene transfer for improved adoptive immunotherapy of cancer (2011)

Adoptive immunotherapy is an appealing approach to cancer treatment, with the potential for more precise targeting and reduced toxicity. While early clinical trial data using adoptive T cells against post-transplant virus-associated hematologic malignancies, lymphoma and melanoma have been promising, treating other solid tumors has proven to be more challenging. Adoptive lymphocytes have been genetically modified in many ways to improve activity and circumvent tumor evasion, including transfer of transgenic T-cell receptors and chimeric antigen receptors to redirect T cell and natural killer cell antigen specificity. Gene transfer may also allow expression of homeostatic cytokines or their receptors to overcome the lack of stimulatory signals or expression of dominant-negative receptors for inhibitory cytokines to compensate for an immunosuppressive tumor milieu. In addition, suicide genes can install a 'safety switch' on adoptively transferred cells to allow ablation if necessary. Although further refinement and validation are necessary, these genetic modification strategies offer hope for significant improvements in cancer immunotherapy.
Three‐point dixon technique for true water/fat decomposition with B0 inhomogeneity correction (1991)

An enhancement to Dixon's technique is described which can provide error-free decomposition of water and fat proton images even in the presence of off-resonance conditions which result from susceptibility differences, demagnetization, or shim errors. The method uses three measurements with phase shifts of 0, pi, and -pi between the fat and water resonances. The additional information provided by the third measurement is used to calculate an image of the field inhomogeneity in addition to true water and fat images. The signal-to-noise ratio (SNR) in the decomposed images is equivalent to that of a 2.7 NEX acquisition (instead of 3 NEX), yielding an SNR imaging efficiency of 95%. In addition, the B0 image which is provided may have diagnostic value in its own right. Examples of head and body scans often portray surprisingly large B0 shifts near interfaces between air or bone and soft tissue.
Quantitation of proteinuria by the use of protein-to-creatinine ratios in single urine samples. (1987)

Measurements of protein-to-creatinine ratios in single-voided urine samples were compared with 24-hour urinary protein excretions for quantitation of proteinuria in inpatients and outpatients. Patients included those representing a broad spectrum of renal diseases, a wide range of proteinuria, and various degrees of reduction in glomerular filtration rate. Protein-to-creatinine ratios in single-voided urine samples correlated well with measurements of 24-hour urinary protein. This simple single-voided test is reliable and useful in the screening, assessment, and follow-up of proteinuria and avoids the problems associated with 24-hour urine collection.
Calcium-Dependent Proteolysis in Rabbit Lens Epithelium after Oxidative Stress (1998)

The purpose of this study was to examine changes in calcium-dependent proteolytic activity in the lens epithelium from whole rabbit lenses exposed to long-term oxidative stress at near physiological levels. Rabbit lenses, incubated in 50 microM H2O2 for 1 or 24 h, were checked for clarity and morphological changes in the epithelium. Proteolytic activity was measured in the epithelium using a fluorogenic synthetic substrate; N-succinyl-Leu-Tyr-7-amino-4-methylocoumarin, both in the presence and the absence of calcium (1 mM Ca2+ and 5 mM EDTA respectively). The effect on transparency and morphology of the epithelium following a 1-hour incubation in 100 microM H2O2 was also studied. Lenses incubated in 50 microM H2O2 were clear even after 24h. After a 1-hour incubation in 50 microM H2O2 the epithelium of the exposed lens appeared normal. However, after 24 h the epithelium cells appeared swollen and microscopical examination showed extensive intracellular and subepithelial vacuolization. Incubation in 100 microM H2O2 for 1 h caused loss of transparency; vacuole formation, globulization of the superficial lens fibers and death of the epithelial cells. There was a 55% increase in calcium-dependent proteolytic activity after 1 h in 50 microM H2O2, implying a role for the calcium-activated protease calpain in oxidatively induced cataract.
On‐line isotachophoretic preconcentration and gel electrophoretic separation of sodium dodecyl sulfate‐proteins on a microchip (2005)

A microchip for integrated isotachophoretic (ITP) preconcentration with gel electrophoretic (GE) separation to decrease the detectable concentration of sodium dodecyl sulfate (SDS)-proteins was developed. Each channel of the chip was designed with a long sample injection channel to increase the sample loading and allow stacking the sample into a narrow zone using discontinuous ITP buffers. The pre-concentrated sample was separated in GE mode in sieving polymer solutions. All the analysis steps including injection, preconcentration, and separation of the ITP-GE process were performed continuously, controlled by a high-voltage power source with sequential voltage switching between the analysis steps. Without deteriorating the peak resolution, four SDS-protein analyses with integrated ITP-GE system resulted in a decreased detectable concentration of approximately 40-fold compared to the GE mode only. A good calibration curve for molecular weights of SDS-proteins indicated that the integrated ITP-GE system can be used for qualitative analysis of unknown protein samples.
Magnetic resonance diffusion characteristics of histologically defined prostate cancer in humans (2009)

The contrast provided by diffusion-sensitive magnetic resonance offers the promise of improved tumor localization in organ-confined human prostate cancer (PCa). Diffusion tensor imaging (DTI) measurements of PCa were performed in vivo, in patients undergoing radical prostatectomy, and later, ex vivo, in the same patients' prostatectomy specimens. The imaging data were coregistered to histological sections of the prostatectomy specimens, thereby enabling unambiguous characterization of diffusion parameters in cancerous and benign tissues. Increased cellularity, and hence decreased luminal spaces, in peripheral zone PCa led to approximately 40% and 50% apparent diffusion policy (ADC) decrease compared with benign peripheral zone tissues in vivo and ex vivo, respectively. In contrast, no significant diffusion anisotropy differences were observed between the cancerous and noncancerous peripheral zone tissues. However, the dense fibromuscular tissues in prostate, such as stromal tissues in benign prostatic hyperplasia in central gland, exhibited high diffusion anisotropy. A tissue classification method is proposed to combine DTI and T2-weighted image contrasts that may provide improved specificity of PCa detection over T2-weighted imaging alone. PCa identified in volume rendered MR images qualitatively correlates well with histologically determined PCa foci.
NAD+-dependent ADP-ribosylation of T Lymphocyte Alloantigen RT6.1 Reversibly Proceeding in Intact Rat Lymphocytes (1995)

Rat T lymphocyte alloantigen 6.1 (RT6.1), which was synthesized as the fusion protein with a maltose-binding protein in Escherichia coli, displayed NAD(+)-dependent auto-ADP-ribosylation in addition to an enzyme activity of NAD+ glycohydrolase. Such ADP-ribosylation of RT6.1 was also observed in lymphocytes isolated from rat tissues as follows. When intact rat lymphocytes expressing RT6.1 mRNA were incubated with [alpha-32P]NAD+, its radioactivity was incorporated into a cell surface protein with the M(r) of 31,000. The radiolabeled 31-kDa protein was released from the cell surface by treatment of the cells with phosphatidylinositol-specific phospholipase C and immunoprecipitated with anti-RT6.1 antiserum. The radioactivity incorporated into the 31-kDa protein was recovered as 5'-[32P]AMP upon incubation with snake venom phosphodiesterase and also removed by NH2OH treatment. These results suggested that the NAD(+)-dependent modification of the 31-kDa protein was due to ADP-ribosylation of glycosylphosphatidylinositol-anchored RT6.1 at an arginine residue. When intact lymphocytes, in which RT6.1 had been once modified by [32P]ADP-ribosylation, were further incubated in the absence of NAD+, there was reduction of the radioactivity in the [32P]ADP-ribosylated RT6.1. The reduced radioactivity was recovered from the incubation medium as [32P]ADP-ribose. This reduction was effectively inhibited by the addition of ADP-ribose to the reaction mixture. Moreover, readdition of NAD+ caused the ADP-ribosylation of RT6.1 again. Thus, the ADP-ribosylation of RT6.1 appeared to proceed reversibly in intact rat lymphocytes.
Neutral Nickel(II)-Based Catalysts for Ethylene Polymerization (1998)

Neutral salicylaldiminato Ni(II) complexes have been synthesized, and their structure has been confirmed by an X-ray analysis of complex 4e. These compounds are active catalysts for the polymerization of ethylene under mild conditions in the presence of a phosphine scavenger such as Ni(COD)2 or B(C6F5)3.