gebhart/patrepeval huggingface dataset:
Performance of an ultrasonic telemetry positioning system under varied environmental conditions (2014)

Advances in ultrasonic telemetry, including the ability to accurately position a transmitter within an array of hydrophone receivers, have led to increased opportunities to investigate a broad spectrum of ecological questions in aquatic systems. The quality and efficiency of positioning a transmitter relies upon factors controlled by the researcher (for example, geometry of the receiver array) as well as environmental conditions (for example, water quality or environmental noise). While the physics of sound wave propagation are well understood, the high amount of environmental variability in and among aquatic habitats makes it difficult to predict exactly how any given ultrasonic signal will behave. To evaluate variability in system performance across different receiver arrays in diverse environments we present positional records for fixed-location tags recorded with a popular positioning array, the VEMCO Positioning System (VPS). Using these records we evaluate the relationships between system performance, measured as both horizontal positioning error and positioning efficiency, and user-controlled and environmental variables. We used generalized linear mixed models to assess performance at a coastal site, a site in a freshwater tidal estuary, and a riverine site. The positioning errors were similar across sites, with median errors ranging from 1.6 to 3.3 m. In contrast, there was large variation in positioning efficiency across sites, with poor positioning efficiency in the coastal habitat (7%), possibly due to high levels of bioacoustic noise, and moderate efficiency in the river (21%) and estuary habitats (27%). Our statistical models indicate that array geometry was consistently the most important predictor of positioning performance. Environmental noise and water movement also emerged as additional predictors of performance at several sites. The results provide insight into VPS performance capabilities and emphasize the importance of testing array geometries. Additionally, water quality parameters should be monitored and receiver mooring designs should be carefully considered before embarking upon a telemetry study. We hope this work will guide future researchers in creating more effective designs for positioning arrays, and facilitate the collection of high quality information about movement and behavior patterns of aquatic organisms.
[<sup>3</sup>H]L-<i>N</i><sup>G</sup>-Nitroarginine Binding after Transient Focal Ischemia and NMDA-Induced Excitotoxicity in Type I and Type III Nitric Oxide Synthase Null Mice (1997)

We investigated the density and distribution of nitric oxide synthase (NOS) binding by quantitative autoradiography using [3H]L-NG-nitroarginine ([3H]L-NNA) after transient focal ischemia or intrastriatal injection of N-methyl-D-aspartate (NMDA) in wild-type (SV-129 and C57black/6) and type I (neuronal) and type III (endothelial) NOS-deficient mice. The middle cerebral artery (MCA) was occluded by an intraluminal filament for 3 h followed by 10 min to 7 days of reperfusion. Specific [3H]L-NNA binding, observed in the wild-type and type III mutant mouse at baseline, increased by 50-250% in the MCA territory during ischemia and the first 3 h of reperfusion. The density of binding sites (Bmax), but not the dissociation constant (Kd), increased significantly during the ischemic period as did type I NOS mRNA as detected by quantitative reverse transcription polymerase chain reaction. [3H]L-NNA binding after intrastriatal NMDA injection also increased by 20-230%. In the type I NOS-deficient mouse, [3H]L-NNA binding was low and only a very small increase was observed after ischemia or excitotoxicity. Under conditions of this study, [3H]L-NNA did not bind to type II NOS as there was no difference in the distribution or density of [3H]L-NNA binding in the rat spleen obtained after lipopolysaccharide treatment despite induction of NOS type II catalytic activity. Our data suggest that an ischemic/excitotoxic insult up-regulates type I NOS gene expression and [3H]L-NNA binding and that this up-regulation may play a pivotal role in the pathogenesis of ischemic/excitotoxic diseases.
Suppression of squamous cell carcinoma growth and differentiation by retinoids. (1994)

The epithelium of the oral cavity is mostly nonkeratinizing. However, it undergoes an abnormal squamous differentiation with keratinization during vitamin A deficiency or oral carcinogenesis. Vitamin A analogues (retinoids) were found to be effective in preventing oral premalignant lesions and second primary cancers in the upper aerodigestive tract. Further development of retinoids for prevention and therapy of squamous cell carcinoma (SCC) requires a better understanding of their mechanism action on the growth and differentiation of SCC cells. We used cultured head and neck SCC (HNSCC) cell lines as a model system. Treatment of HNSCC cells with beta-all-trans-retinoic acid resulted in inhibition of growth (proliferation and colony formation) and suppression of squamous differentiation to varying degrees in the different cell lines. Because some of the malignant HNSCC cells recapitulate the main characteristics of keratinocyte squamous differentiation and responsiveness to retinoids, they can serve as a model for investigating the mechanism underlying the effects of retinoids on cell growth and differentiation. It is thought that nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs) mediate the above effects of retinoids by acting as DNA-binding transcription-modulating factors. We found that HNSCC cell lines express several nuclear RAR and that their level could be modulated by retinoids in some cell lines. An inverse relationship was found between RAR-beta expression and squamous differentiation. An analysis of RAR mRNA expression in head and neck cancer specimens revealed a decrease in RAR-beta in premalignant and malignant tissues relative to normal mucosa. The expression of this receptor increased in vivo after treatment with 13-cis-retinoic acid. These results implicate the loss of RAR-beta expression in the development of head and neck cancer and suggest that RAR-beta could serve as an intermediate marker in prevention trials.
Quantification of gas bubble emissions from submarine hydrocarbon seeps at the Makran continental margin (offshore Pakistan) (2012)

Evidence for twelve sites with gas bubble emissions causing hydroacoustic anomalies in 18 kHz echosounder records (‘flares’) was obtained at the convergent Makran continental margin. The hydroacoustic anomalies originating from hydrocarbon seeps at water depths between 575 and 2870 m disappeared after rising up to 2000 m in the water column. Dives with the remotely operated vehicle ‘Quest 4000 m’ revealed that several individual bubble vents contributed to one hydroacoustic anomaly. Analyzed gas samples suggest that bubbles were mainly composed of methane of microbial origin. Bubble size distributions and rise velocities were determined and the volume flux was estimated by counting the emitted bubbles and using their average volume. We found that a low volume flux (Flare 1 at 575 mbsl: 90 ml/min) caused a weak hydroacoustic signal in echograms whereas high volume fluxes (Flare 2 at 1027 mbsl: 1590 ml/min; Flare 5 C at 2870 mbsl: 760 ml/min) caused strong anomalies. The total methane bubble flux in the study area was estimated by multiplying the average methane flux causing a strong hydroacoustic anomaly in the echosounder record with the total number of equivalent anomalies. An order‐of‐magnitude estimate further considers the temporal variability of some of the flares, assuming a constant flux over time, and allows a large range of uncertainty inherent to the method. Our results on the fate of bubbles and the order‐of‐magnitude estimate suggest that all of the ∼40 ± 32 × 10 6 mol methane emitted per year within the gas hydrate stability zone remain in the deep ocean.
Properties of strains of<i>Escherichia coli</i>belonging to serogroup O 157 with special reference to production of Vero cytotoxins VTl and VT2 (1987)

Fifty-four strains of Escherichia coli belonging to serogroup O157 were examined for the production of Vero cytotoxins VT1 and VT2, and for other properties such as plasmid content, resistance to antimicrobial agents and colicin production. Twenty-six strains from cases of diarrhoea, haemorrhagic colitis and haemolytic uraemic syndrome in humans produced VT. By serum neutralization tests and hybridization with DNA probes for VT1 or VT2, three classes were recognized which produced either VT1 alone or VT2 alone or both VT1 and VT2. These strains were of H type 7 or non-motile. The strains producing VT were sensitive to all the antimicrobial agents tested, and all carried at least one plasmid which had a molecular weight of c. 60 X 10(6). Seven strains of porcine origin and 21 strains of human origin did not produce VT or hybridize with either DNA probe. None of these strains was of H type 7. Of the 21 human VT- strains, 17 were of extra-intestinal origin and 18 were of H type 45. Twenty-three of the 28 VT-strains were resistant to at least one antimicrobial agent.
Association of killer cell immunoglobulin‐like receptors with scleroderma (2004)

The genetic combination of KIR2DS2+ and KIR2DL2- is associated with scleroderma.
Security Analysis of salt||password Hashes (2012)

Protection of passwords used to authenticate computer systems and networks is one of the most important application of cryptographic hash functions. Due to the application of precomputed memory look up attacks such as birthday and dictionary attacks on the hash values of passwords to find passwords, it is usually recommended to apply hash function to the combination of both the salt and password, denoted salt||password, to prevent these attacks. In this paper, we present the first security analysis of salt||password hashing application. We show that when hash functions based on the compression functions with easily found fixed points are used to compute the salt||password hashes, these hashes are susceptible to precomputed offline birthday attacks. For example, this attack is applicable to the salt||password hashes computed using the standard hash functions such as MD5, SHA-1, SHA-256 and SHA-512 that are based on the popular Davies-Meyer compression function. This attack exposes a subtle property of this application that although the provision of salt prevents an attacker from finding passwords, salts prefixed to the passwords do not prevent an attacker from doing a precomputed birthday attack to forge an unknown password. In this forgery attack, we demonstrate the possibility of building multiple passwords for an unknown password for the same hash value and salt. Interestingly, password||salt (i.e. salts suffixed to the passwords) hashes computed using Davies-Meyer hash functions are not susceptible to this attack, showing the first security gap between the prefix-salt and suffix-salt methods of hashing passwords.
Pyrazolopyrimidine nucleosides. Part VIII The synthesis of certain 4‐substituted pyrazolo[3,4‐<i>d</i>]pyrimidine nucleosides (1977)

Abstract 1‐(β‐D‐Ribofuranosyl)pyrazolo[3,4‐ b ]pyrimidine‐4‐thione ( 6 ), obtained by a three‐step synthesis from allopurinol riboside (3), was treated with certain alkyl and aryl halides to provide the corresponding 4‐alkylthio derivatives. The nucleoside 4‐methylthio‐1‐(β‐D‐ribofuranosyl)pyra‐zolo[3,4‐ d ]pyritnidine ( 7 ) has served as the precursor for the preparation of the 4‐methylamino ( 11 ), 4‐dimethylamino ( 12 ), 4‐hydrazino ( 13 ), and the 4‐hydroxylamino ( 14 ) analogs.
A low-cost PC-oriented virtual environment for operator training (1998)

Virtual environment (VE) technologies have been shown to provide invaluable training in the performance of complex procedural tasks. Of paramount importance to the success of any VE is realism; entities must move and behave believably and approximate the complexity of the real world. Such real-world fidelity is accompanied by the challenge of making immersive training in virtual reality (VR) more widely available, at costs significantly less prohibitive. A solution is presented to recreate the VE on low-cost PCs, reducing the cost of the VR software itself, yet preserving real-time performance. This paper presents a low-cost, PC-based VR development system within the framework of ESOPE-VR, a VR operator training simulator (OTS) prototype for power-utility personnel. PC-ESOPE-VR aims to provide the same or improved functionality and performance as the original, with a 3-D visual interface, voice recognition and feedback, navigation and manipulation facilities, and expert system, multimedia and multi-user (distributed) support, yet address the practical demands raised above. The PC-based system is also compatible with the original; it can draw on existing ESOPE-VR power component libraries and support the automatic synthesis of a virtual power station environment from its single-line diagram representation. The approach used towards fulfilling all these issues is described, followed by key implementation results.
Interaction of TorsinA with Its Major Binding Partners Is Impaired by the Dystonia-associated ΔGAG Deletion (2009)

Early onset (DYT1) torsion dystonia is a dominantly inherited movement disorder associated with a three-base pair (DeltaGAG) deletion that removes a glutamic acid residue from the protein torsinA. TorsinA is an essential AAA(+) (ATPases associated with a variety of cellular activities) ATPase found in the endoplasmic reticulum and nuclear envelope of higher eukaryotes, but what it does and how changes caused by the DeltaGAG deletion lead to dystonia are not known. Here, we asked how the DYT1 mutation affects association of torsinA with interacting proteins. Using immunoprecipitation and mass spectrometry, we first established that the related transmembrane proteins LULL1 and LAP1 are prominent binding partners for torsinA in U2OS cells. Comparative analysis demonstrates that these two proteins are targeted to the endoplasmic reticulum or nuclear envelope by their divergent N-terminal domains. Binding of torsinA to their C-terminal lumenal domains is stabilized when residues in any one of three motifs implicated in ATP hydrolysis (Walker B, sensor 1, and sensor 2) are mutated. Importantly, the DeltaGAG deletion does not stabilize this binding. Indeed, deleting the DeltaGAG encoded glutamic acid residue from any of the three ATP hydrolysis mutants destabilizes their association with LULL1 and LAP1C, suggesting a possible basis for loss of torsinA function. Impaired interaction of torsinA with LULL1 and/or LAP1 may thus contribute to the development of dystonia.
Prevention of Hypoglycemia Using Risk Assessment With a Continuous Glucose Monitoring System (2002)

Due to the lag between sugar intake and the beginning of recovery from hypoglycemia, it is necessary to intervene in an anticipatory way if one wants to prevent, not only detect, hypoglycemia. This article presents the principle of a hypoglycemia prevention system based on risk assessment. The risk situation can be defined as the moment when the system estimates that the glucose concentration is expected to reach a hypoglycemia threshold in less than a given time (e.g., 20 min). Since there are well-known discrepancies between blood and interstitial glucose concentrations, the aim of this experimental study performed in nondiabetic rats was first to validate this strategy, and second to determine whether it can work when the glucose concentration is estimated by a glucose sensor in subcutaneous tissue rather than in blood. We used a model of controlled decrease in blood glucose concentration. A glucose infusion, the profile of which mimicked the appearance of glucose from an intragastric load, was administered either when hypoglycemia was detected or on the basis of risk recognition. Despite the lag between the beginning of the load and that of the increase in blood glucose concentration, which was in all experiments 15-20 min, hypoglycemia was fully prevented without overshoot hyperglycemia in the groups of rats in which the glucose load was started when the hypoglycemia risk was detected, on the basis of either blood or interstitial glucose concentration. This was, of course, not the case when the same glucose load was infused at the detection of the hypoglycemia threshold.
Can Dexter cultures support stem cell proliferation? (1992)

The in vitro culture of mouse bone marrow (Dexter cultures) has allowed a detailed analysis of the biology of murine hematopoiesis. However, attempts to develop stable long-term human bone marrow cultures have been unsuccessful. Available culture systems all have finite and relatively short lifetimes. The reasons for the limited longevity are unknown. Utilizing computer-assisted integration techniques, we have theoretically simulated culture cell production kinetics to help identify factors that may be responsible for culture decay, as well as to suggest possible means of improving culture longevity. The simulation demonstrates that removal of stem cells is a possible mechanism leading to culture decline. Under the standard bone marrow culture conditions, even with a high stem cell renewal rate, the cultures appear to be destined to fail. Thus, the development of proper sampling techniques or improved stem cell retention may be critical to obtain successful long-term cultures.
Weak inversion MOS varactors for 0.5 V analog integrated filters (2005)

This work proposes a weak-inversion MOS capacitor-based varactor, tuned through the body voltage, for the realization of tunable filters at supply voltages down to 0.5 V. Weak inversion operation results in a distributed series resistance and a model is derived to accurately calculate this frequency dependent resistance. The model matches well with experimental results from test devices in a 0.18 /spl mu/m CMOS technology. Channel segmentation is used to simulate the varactor. Use of the varactor is demonstrated in the design of tunable filters and good agreement is obtained between simulated and measured performance.
Chemotherapy for advanced non-small cell lung cancer: past, present, and future. (1997)

Until recently, chemotherapeutic intervention in advanced and metastatic non-small cell lung cancer (NSCLC) has been viewed with a certain degree of nihilism. Although meta-analysis of randomized clinical studies from the 1970s and 1980s comparing cisplatin-based chemotherapy to best supportive care in metastatic NSCLC showed improvement in survival, it was modest at best. A number of novel agents have been developed with significant activity against NSCLC in the past 5 to 6 years and are being incorporated into the therapy of this disease. These agents include paclitaxel, docetaxel, vinorelbine, gemcitabine, and irinotecan. Clearly there has been improvement in response rates, and in some cases the responses have been durable with an increase in the number of 1- and 2-year survivors. The next generation of studies has evaluated combinations of these novel agents with either cisplatin or carboplatin for patients with NSCLC and the results have been provocative, with 1-year survival rates as high as 54%. A randomized phase III study of the Eastern Cooperative Oncology Group has shown the superiority of paclitaxel-cisplatin regimens over etoposide-cisplatin for patients with advanced and metastatic NSCLC. The vinorelbine-cisplatin regimen has also proven to have significant, albeit modest benefit in survival when compared with cisplatin alone. These combination regimens have now become the reference regimens in ongoing randomized studies. There is continued interest in developing new agents, or selective approaches that effect novel targets with the hope of showing improved therapeutic activity. Some of these approaches include gene therapy, monoclonal antibodies, and introduction of antisense oligodeoxynucleotides. With better understanding of the molecular and cellular biology of lung cancer, the hope for the future is to combine the mechanistic approaches with new drug development to define an effective, optimal, and definitive regimen for NSCLC.
Silencing of the Escherichia Coli bgl Promoter: Effects of Template Supercoiling and Cell Extracts on Promoter Activity in vitro (1996)

Regulation of the Escherichia coli bgl promoter involves the catabolite gene activator protein (CAP) and silencer elements that are located upstream and downstream of the promoter and its CAP binding site. The promoter is kept in a repressed state by the silencer elements and other normally active CAP-dependent or -independent promoters are repressed as well when flanked by these elements. To assess the mechanism of promoter repression, single round in vitro transcription was carried out with plasmids bearing either the wild-type bgl promoter or one of two derivatives that escape repression in vivo by different mechanisms: C234 by improving the CAP binding site of the promoter and delta1 by a deletion within the upstream silencer sequence. Repression of the bgl promoter in vitro was shown to depend on template topology and the presence of cellular factors. With negatively supercoiled templates, all three promoters are transcribed to similar extents by purified E. coli RNA polymerase and no CAP dependence is apparent; with relaxed templates, transcription is CAP dependent, but the levels of transcription of the three promoters are comparable. Addition of crude cell extract to the simple transcription system leads to repression of all three promoter alleles in the absence of CAP. Repression of the mutant alleles but not of the wild-type promoter is completely relieved in the presence of the CAP-cAMP complex. The topology of the DNA template is also important in the differential regulation of these promoters. In the case of C234, repression by cell extract is completely relieved by CAP-cAMP on relaxed or negatively supercoiled templates, while complete derepression of delta1 by CAP-cAMP occurs on negatively supercoiled templates only. Repression by cell extract requires the presence of the histone-like protein H-NS. However, H-NS alone does not appear to be sufficient for specific silencing of the wild-type promoter, since repression of all three promoter alleles caused by purified H-NS protein is completely relieved by the CAP-cAMP complex. These data suggest that template topology, H-NS and other cellular factors are involved in the formation of a specific nucleoprotein structure in the bgl promoter-silencer region; the formation of this nucleoprotein structure keeps an otherwise active promoter in an inactive state.
Fusion: a Visualization Framework for Interactive Ilp Rule Mining With Applications to Bioinformatics (2004)

Microarrays provide biologists an opportunity to find the expression profiles of thousands of genes simultaneously. Biologists try to understand the mechanisms underlying the life processes by finding out relationships between gene-expression and their functional categories. Fusion is a software system that aids the biologists in performing microarray data analysis by providing them with both visual data exploration and data mining capabilities. Its multiple view visual framework allows the user to choose different views for different types of data. Fusion uses Proteus, an Inductive Logic Programming (ILP) rule finding algorithm to mine relationships in the microarray data. Fusion allows the user to explore the data interactively, choose biases, run the data mining algorithms and visualize the discovered rules. Fusion has the capability to smoothly switch across interactive data exploration and batch data mining modes. This optimizes the knowledge discovery process by facilitating a synergy between the interactivity and usability of visualization process with the pattern-finding abilities of ILP rule mining algorithms. Fusion was successful in helping biologists better understand the mechanisms underlying the acclimatization of certain varieties of Arabidopsis to ozone exposure.