gebhart/patrepeval huggingface dataset:
Design of a Conformationally Defined and Proteolytically Stable Circular Mimetic of Brain-derived Neurotrophic Factor (2008)

Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophin family of neurotrophic factors. BDNF has long been recognized to have potential for the treatment of a variety of human neurodegenerative diseases. However, clinical trials with recombinant BDNF have yet to yield success, leading to the suggestion that alternative means of harnessing BDNF actions for therapeutic use may be required. Here we describe an approach to create low molecular weight peptides that, like BDNF, promote neuronal survival. The peptides were designed to mimic a cationic tripeptide sequence in loop 4 of BDNF shown in previous studies to contribute to the binding of BDNF to the common neurotrophin receptor p75NTR. The best of these peptides, the cyclic pentapeptide 2 (cyclo(-D-Pro-Ala-Lys-Arg-)), despite being of low molecular weight (Mr 580), was found to be an effective promoter of the survival of embryonic chick dorsal root ganglion sensory neurons in vitro (maximal survival, 68 +/- 3% of neurons supported by BDNF). Pentapeptide 2 did not affect the phosphorylation of either TrkB (the receptor tyrosine kinase for BDNF) or the downstream signaling molecule MAPK, indicating that its mechanism of neuronal survival action is independent of TrkB. NMR studies reveal that pentapeptide 2 adopts a well defined backbone conformation in solution. Furthermore, pentapeptide 2 was found to be effectively resistant to proteolysis when incubated in a solution of rat plasma in vitro. These properties of pentapeptide 2 (low molecular weight, appropriate pharmacological actions, a well defined solution conformation, and proteolytic stability) render it worthy of further investigation, either as a template for the further design of neuronal survival promoting agents or as a lead compound with therapeutic potential in its own right.
The meaning and importance of drug potency in medicine (1966)

The term “potency” is ambiguous, because it may refer to the quantity of drug necessary to produce a given effect, or it may refer to the maximum response which can be achieved with the drug. In the first sense, cyclopenthiazide is more potent than frusemide, and in the second sense the reverse is true. Potency cannot be measured in precise and absolute terms without detailed specification of the method of measurement, and then it becomes an excessively arbitrary measurement. Relative potency is more easily determined, but it also is variable according to the circumstances in which it is assessed. An approximate estimate of potency is afforded by the dose ordinarily used therapeutically. For some groups of drugs, variation in effective dose is enormous and for others, quite small. The causes of such variations are not well known, but probably involve the cumulation of several separate factors. Differences in maximal effect generally indicate a different mode of action and raise doubts about the strict comparability of the drugs concerned. Such differences have definite therapeutic utility. Otherwise high potency (in the sense of small effective dosage) has some advantages and some disadvantages to a therapist and is, at best, a minor merit in most circumstances.
An Outstandingness Oriented Image Segmentation and its Application (1996)

This paper presents a novel automatic method to determine region importance, and its application to still image compression. We use fuzzy technique to determine important regions in the same manner as human beings do, allocate higher bitrate to important regions while lower to the rest parts of image. Therefore, it allows both higher quality of important parts and lower bitrate as a whole, and it reflects the sense of human beings. The paper mainly introduces the important region determination, briefly on importance adaptive image codec, and finally gives experimental results.
The Psychology of Safety (2011)

Many studies of mishaps show that human error is a factor in a significant majority of accidents. Trying to decide how to change human behavior to be safer is generally the biggest challenge of any safety program. However, understanding the human psyche is the first step to changing behavior. Many studies focus on the before and after of an accident, but what about the thoughts of a person in the commission of an unsafe act? This is a less understood area. Examining it reveals why it is not well comprehended. This paper attempts to examine a part of the thought process, with an eye to helping influence people to less hurtful actions.
A Black-Box Self-Learning Scheduler for Cloud Block Storage Systems (2016)

A major requirement of cloud block storage services is guaranteed performance and high availability. However, offering guaranteed Service Level Agreements (SLAs) in cloud block storage services is often not straightforward. Cloud block storage performance may be affected by physical disk background operations, like garbage collection, storage cluster features, workload interference and the chraracteristcs of the workload itself. On the other hand, the underlying physical storage drives do not expose the internal states to higher level block storage service offerings. Therefore, SLAs can only be satisfied by over-provisioning the storage resources. To address this issue, we propose a self-learning scheduler that can dynamically adapt based on the workload, and efficiently provide a scheduling decision with zero knowledge of the underlying hardware. We study two candidate algorithms based on Feedback learning and Two-Phase learning. We used workloads that were deducted from real-world block-level traces of an enterprise data center, and conducted extensive simulations. Our results indicate that the self-learning scheduling approach can reduce the SLA violations by mitigating the unexpected resource fluctuation, and the scheduler can also adapt dynamically to various workloads.
Comparison of the mutagenic and clastogenic activity of amsacrine and other DNA-intercalating drugs in cultured V79 Chinese hamster cells. (1984)

The acridine derivative amsacrine (m-AMSA) is used clinically for the treatment of acute leukemias. The mutagenic activity of this drug has been evaluated at the 6-thioguanine (6-TG) and ouabain resistance loci in cultured Chinese hamster fibroblasts (V79-171b cell line). m-AMSA was found to have weak but significant mutagenic activity at the 6-TG but not at the ouabain resistance locus, after either 1- or 45-hr exposures at concentrations causing up to 90% cell kill. Two other intercalating agents with antitumor activity, Adriamycin and actinomycin D, provided essentially identical results. All three drugs were potent inducers of micronuclei in V79-171b cells, indicating high clastogenic activity. For these intercalating agents, the yield of 6-TG-resistant mutants was approximately 100-fold lower than that for ethyl methanesulfonate after exposures causing equivalent toxicity or equivalent chromosome breakage. The acridine half-mustard ICR-191 resembled ethyl methanesulfonate rather than the other intercalating agents in providing a high yield of 6-TG-resistant mutants relative to its clastogenic activity. The tumor-inactive intercalator 9-aminoacridine demonstrated only low clastogenic activity with a lack of significant mutagenic activity at toxic concentrations. These results suggest that, for m-AMSA, Adriamycin, and actinomycin D, both cell killing and mutagenesis could be direct consequences of chromosome breakage, while 9-aminoacridine may kill cells by a different mechanism. In view of its mutagenic and clastogenic activity at clinically achievable exposures and the similarity of its genotoxic properties to Adriamycin, m-AMSA should be considered a potential carcinogen.
Modulation of sweet taste sensitivity by orexigenic and anorexigenic factors (2010)

The present study summarized recent findings on roles of leptin and endocannabinoids as modulators of the peripheral components of sweet taste. The positive effect of endocannabinoids on sweet sensitivity was opposed to that of leptin which suppresses sweet sensitivity. Leptin and endocannabinoids, therefore, not only regulate food intake via central nervous systems but also may modulate palatability of foods by altering peripheral sweet taste responses via their cognate receptors. Orexigenic and anorexigenic factors such as endocannnabinoids and leptin may affect energy homeostasis by regulating taste sensitivity.
Performance of the nonlinear joint transform correlator for images with low-pass characteristics (1994)

The correlation performance of the nonlinear joint transform correlator for input images containing a target embedded in input noise is investigated. We focus on a class of images for the target, the input image, and the input noise for which nonlinear joint transform correlators perform well. The target and the input noise have low-pass characteristics; that is, they are not band limited but have most of their energies in the low spatial frequency domain. The analytical results show that for this class of low-pass (but not band-limited) images, the binary joint transform correlator outperforms other types of kth-law nonlinear joint transform correlators with k ≠ 0 when the input-noise bandwidth is less than the target bandwidth. We show that binary nonlinear joint transform correlators perform well when the input noise is signallike; that is, the input noise or the objects to be rejected have energy spectra that are similar to the target energy spectrum. Correlation tests with computer simulations are prese ted. The nonlinear joint transform correlator performance is determined for various degrees of nonlinear transformations and for different input-noise parameters. For the nonlinear joint transform correlator the correlation-signal term and the output-noise term arising from the input noise are determined for various degrees of nonlinearity for the target embedded in input noise.
TreeMAC: Localized TDMA MAC protocol for real-time high-data-rate sensor networks (2009)

Earlier sensor network MAC protocols focus on energy conservation in low-duty cycle applications, while some recent applications involve real-time high-data-rate signals. This motivates us to design an innovative localized TDMA MAC protocol to achieve high throughput and low congestion in data collection sensor networks, besides energy conservation. TreeMAC divides a time cycle into frames and frame into slots. Parent determines children's frame assignment based on their relative bandwidth demand, and each node calculates its own slot assignment based on its hop-count to the sink. This innovative 2-dimensional frame-slot assignment algorithm has the following nice theory properties. Firstly, given any node, at any time slot, there is at most one active sender in its neighborhood (including itself). Secondly, the packet scheduling with TreeMAC is bufferless, which therefore minimizes the probability of network congestion. Thirdly, the data throughput to gateway is at least 1/3 of the optimum assuming reliable links. Our experiments on a 24 node test bed demonstrate that TreeMAC protocol signi ficantly improves network throughput and energy efficiency, by comparing to the TinyOS's default CSMA MAC protocol and a recent TDMA MAC protocol Funneling-MAC.
Reduction of the chromatic dispersion penalty at 10 Gbit/s by integrated electronic equalisers (2002)

At 10 Gbit/s a 3.3 dB reduction of the power penalty induced by the chromatic dispersion of an 127 km standard single-mode fiber (G.652) has been achieved (BER=10/sup -9/, PRBS 2/sup 23/-1) by processing the detected signal in the receiver with a nonlinear equaliser realized as SiGe integrated circuit.
Role of M protein in pharyngeal colonization by group A streptococci in rats (1993)

As the initial step in infection, group A streptococci (GAS) colonize either the nasopharyngeal mucosa or the skin of humans. A number of virulence factors have been implicated in the colonization phase of pathogenesis based upon their in vitro activities, but the in vivo data supporting their role in colonization of the host tissues is lacking. In this investigation, the potential requirement for M protein in pharyngeal colonization by GAS was explored by using near-isogenic strains in experimental animals studies. Fischer rats were infected by intranasal and oral inoculation with both M-positive and M-negative Streptococcus pyogenes strains. Colonization of the pharyngeal area by the streptococci was monitored at various time intervals. Both M-positive and M-negative strains colonized during the first week following infection, indicating that M protein was not necessary for this initial colonization. Two M-positive strains of S. pyogenes were recovered from the rats up to 23 weeks following inoculation, while the colonization levels for M-negative strains decreased rapidly in the second and third weeks, becoming negligible by the fourth week. This indicates a potential role for M protein in the persistence of colonization at this mucosal surface. Colonization of rats with either M-positive strain of S. pyogenes also resulted in the appearance of salivary and serum antibody responses. This in vivo model should allow further investigation into factors required for GAS disease, including the examination of the potential role of the host immune response both in modulation of the pharyngeal surface and in modulation of antigenic changes in M protein or other surface factors.
Limited Liability Companies: A New Tool for Small Agribusinesses? (1997)

Agribusiness
Cross-Validatory Choice of the Number of Components From a Principal Component Analysis (1982)

A method is described for choosing the number of components to retain in a principal component analysis when the aim is dimensionality reduction. The correspondence between principal component analysis and the singular value decomposition of the data matrix is used. The method is based on successively predicting each element in the data matrix after deleting the corresponding row and column of the matrix, and makes use of recently published algorithms for updating a singular value decomposition. These are very fast, which renders the proposed technique a practicable one for routine data analysis.
Structural Brain MRI Segmentation Using Machine Learning Technique (2016)

Segmenting brain MR scans could be highly benecial for diagnosing, treating and evaluating the progress of specic diseases. Up to this point, manual segmentation,performed by experts, is the conventional method in hospitals and clinical environments. Although manual segmentation is accurate, it is time consuming, expensive and might not be reliable. Many non-automatic and semi automatic methods have been proposed in the literature in order to segment MR brain images, but the levelof accuracy is not comparable with manual segmentation. The aim of this project is to implement and make a preliminary evaluation of a method based on machine learning technique for segmenting gray matter (GM),white matter (WM) and cerebrospinal uid (CSF) of brain MR scans using images available within the open MICCAI grand challenge (MRBrainS13).The proposed method employs supervised articial neural network based autocontext algorithm, exploiting intensity-based, spatial-based and shape model-basedlevel set segmentation results as features of the network. The obtained average results based on Dice similarity index were 97.73%, 95.37%, 82.76%, 88.47% and 84.78% for intracranial volume, brain (WM + GM), CSF, WM and GM respectively. This method achieved competitive results with considerably shorter required training time in MRBrainsS13 challenge.
Mechanism responsible for glucose–lactose diauxie in <i>Escherichia coli</i>: challenge to the cAMP model (1996)

We conclude that the repression of beta-galactosidase expression by glucose is not due to the reduction of the cAMP-CRP level but due to an inducer exclusion mechanism which is mediated by the phosphoenolpyruvate-dependent sugar phosphotransferase system.
Web Caching in a Pervasive Computing World (2002)

... are accessing information sources by a huge variety of mobile devices featuring heterogeneous capabilities. Those devices are attached to the Internet by various communication systems offering different quality of service. The key to meet the demands in this heterogeneous environment is the adaptation of contents to the capabilities of the devices and communication systems. However, content adaptation interferes with the effectiveness of web caching applied in the World Wide Web to improve the performance by avoiding redundant data transfers. Leveraging
128-bit multicomparator (1976)

A 128-bit multicomparator was designed to perform the search-sort function on arbitrary length data strings. Devices can be cascaded for longer block lengths or paralleled for bit-parallel, word-serial applications. The circuit utilizes a 3-phase static-dynamic shift register cell for data handling and a unique gated EXCLUSIVE-NOR circuit to accomplish the compare function. The compare operation is performed bit parallel between a `data' register and a `key' register with a third `mask' register containing DON'T CARE bits that disable the comparator. The multicomparator was fabricated using p-channel silicon-gate metal-oxide-semiconductor (MOS) technology on a 107/spl times/150 mil chip containing 3350 devices. With transistor-transistor logic (TTL) input, data rates in excess of 2 MHz have been attained. The average power dissipation was 250 mW in the dynamic mode and 300 mW in the static mode.
Reaction of Prostaglandin Endoperoxide Synthase with cis,cis-Eicosa-11,14-dienoic Acid (1998)

The pre-steady-state phase of the oxygenase reaction of prostaglandin endoperoxide synthase with cis,cis-eicosa-11, 14-dienoic acid has been studied using stopped flow techniques. Because some intermediate forms of prostaglandin endoperoxide synthase are spectrally indistinguishable, the enzyme and substrate transformations were monitored in parallel to simplify the interpretation of the kinetics. Over a wide range of conditions, the formation of the enzyme intermediate II, the form of compound I containing the tyrosyl radical, precedes substrate oxidation. This result supports the occurrence of a unimolecular conversion of compound I into intermediate II. Furthermore, the rate of intermediate II formation was stimulated by increased concentration of dienoic acid, perhaps because of increased occupation of the fatty acid binding site. The importance of the unimolecular formation of intermediate II was confirmed by simulated kinetics of the oxygenase reaction. These results provide evidence that intermediate II is the primary oxidant in the reaction of prostaglandin synthase with the dienoic acid, as it is with arachidonic acid.
Planning and Interpreting NMR Fluid-Characterization Logs (2003)

Abstract This paper presents a logical approach to ensure successful nuclear magnetic resonance (NMR) logging for fluid-characterization purposes. Numerous examples are shown in a three-stage process consisting of a) planning, b) processing and interpretation, and c) validation and integration. First, modeling is performed to assess the NMR contrast, using any available information concerning anticipated fluid types. Knowledge of downhole conditions also allows the estimation of the NMR signal-to-noise ratio (SNR) from which the sensitivity and statistical error can be evaluated. The outcome of the planning process is a suite of NMR pulse sequences that optimizes resolution of the different fluids and minimizes error with the shortest possible acquisition time. Interpreting fluid-characterization NMR logs is relatively straightforward when the fluids have large NMR contrast and obey the standard correlations. However, dissolved gas, wettability variations, internal field gradients, and restricted diffusion can cause deviations from model behavior and have significant effects on NMR relaxation data. These effects need to be recognized and accounted for. To gain insights into the NMR-based fluid evaluation process, we have developed a model-independent technique that gives various sets of D-T1-T2 maps. The maps are analogous to the crossplots commonly used in log interpretation practices and are indispensable in the interpretation of the data. We also explain quantitative interpretation techniques from D-T2 maps. Integrating NMR fluid-characterization results with other information and openhole logs constitutes the final step. As with any technique, results need to be crosschecked with other log data for consistency. The answer gives a water saturation that can be verified with other tools and techniques such as the dielectric log, resistivity logs, and the density magnetic resonance technique method.
Design and implementation of a new digital automatic gain control (2016)

A new design method of an all‐digital automatic gain control easy to implement is described and tested. The discretisation of the instantaneous gain provides a recursive form that merges the exponential function with the level detection. The first proposed circuit is well adapted for a software implementation. It comprises a simple control loop and two multipliers. It does neither contain digital filter nor divider and its setting only requires a loop gain parameter. Some tests were conducted on real digital audio signals with a dynamic range of 80 dB and they validate this approach. Under some conditions, the second circuit can even be simpler since it requires only one multiplier. It is well adapted to an field programmable gate array (FPGA) implementation for high speed signal processing.
Constance (2016)

As the challenge of our time, Big Data still has many research hassles, especially the variety of data. The high diversity of data sources often results in information silos, a collection of non-integrated data management systems with heterogeneous schemas, query languages, and APIs. Data Lake systems have been proposed as a solution to this problem, by providing a schema-less repository for raw data with a common access interface. However, just dumping all data into a data lake without any metadata management, would only lead to a 'data swamp'. To avoid this, we propose Constance, a Data Lake system with sophisticated metadata management over raw data extracted from heterogeneous data sources. Constance discovers, extracts, and summarizes the structural metadata from the data sources, and annotates data and metadata with semantic information to avoid ambiguities. With embedded query rewriting engines supporting structured data and semi-structured data, Constance provides users a unified interface for query processing and data exploration. During the demo, we will walk through each functional component of Constance. Constance will be applied to two real-life use cases in order to show attendees the importance and usefulness of our generic and extensible data lake system.
Regression Testing Ajax Applications: Coping with Dynamism (2010)

There is a growing trend to move desktop applications towards the web using advances made in web technologies such as Ajax. One common way to provide assurance about the correctness of such complex and evolving systems is through regression testing. Regression testing classical web applications has already been a notoriously daunting task because of the dynamism in web interfaces. Ajax applications pose an even greater challenge since the test case fragility degree is higher due to extensive run-time manipulation of the DOM tree and asynchronous client/server interactions. In this paper, we propose a technique, in which we automatically generate test cases and apply pipelined oracle comparators along with generated DOM templates, to deal with dynamic non-deterministic behavior in Ajax user interfaces. Our approach, implemented in Crawljax, is open source and provides a set of generic oracle comparators, template generators, and visualizations of test failure output. We describe two case studies evaluating the effectiveness, scalability, and required manual effort of the approach.