gebhart/patrepeval huggingface dataset:
Dimethylthetin can substitute for glycine betaine as an osmoprotectant molecule for Escherichia coli (1987)

Glycine betaine is believed to be the most active naturally occurring osmoprotectant molecule for Escherichia coli and other bacteria. It is a dipolar ion possessing a quaternary ammonimum group and a carboxylic acid group. To examine the molecular requirements for osmoprotective activity, dimethylthetin was compared with glycine betaine. Dimethylthetin is identical to glycine betaine except for substitution of dimethyl sulfonium for the quaternary nitrogen group. Dimethylthetin was found to be about equally as effective as glycine betaine in permitting E. coli to grow in hypertonic NaCl, and both compounds were recovered almost completely from bacterial cells grown in the presence of hypertonic NaCl. 3-Dimethylsulfonioproprionate, an analog of dimethylthetin observed in marine algae, and 3-Dimethylsulfonio-2-methylproprionate were found to be less active. Dimethylthetin may prove useful as a molecular probe to study betaine metabolism and as a model for the development of antibacterial agents.
Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance (2009)

Microdeletion at chromosomal position 15q13.3 has been described in intellectual disability, autism spectrum disorders, schizophrenia and recently in idiopathic generalized epilepsy (IGE). Using independent IGE cohorts, we first aimed to confirm the association of 15q13.3 deletions and IGE. We then set out to determine the relative occurrence of sporadic and familial cases and to examine the likelihood of having seizures for individuals with the microdeletion in familial cases. The 15q13.3 microdeletion was identified in 7 of 539 (1.3%) unrelated cases of IGE using quantitative PCR or SNP arrays and confirmed by array comparative genomic hybridization analysis using probes specific to the 15q13.3 region. The inheritance of this lesion was tracked using family studies. Of the seven microdeletions identified in probands, three were de novo, two were transmitted from an unaffected parent and in two cases the parents were unavailable. Non-penetrance of the microdeletion was identified in 4/7 pedigrees and three pedigrees included other family members with IGE who lacked the 15q13.3 deletion. The odds ratio is 68 (95% confidence interval 29-181), indicating a pathogenic lesion predisposing to epilepsy with complex inheritance and incomplete penetrance for the IGE component of the phenotype in multiplex families.
Small humanoid robot localization by landmarks (2008)

This paper presents an academic prototype small humanoid robot with vision-system to achieving the posture estimation. With the on-board Personal Digital Assistant (PDA) to in charge of the image processing and then recognize its surroundings. According to the information of the image data from the PDA-based real-time image sensor, the Nios-based motor control chip is employed to achieve the desired motions, including forward walking, backward walking and turning. To navigate the robot, a triangulation method with a CCD camera with three artificial color landmarks is used to determine the robot’s posture using the on-board PDA. An Extended Kalman Filter (EKF) algorithm is employed to improve estimation accuracy of the humanoid robot. Computer simulation and experiment results are conducted to verify the efficacy of the proposed method.
A novel zero overhead obfuscation technique for securing FPGA designs (2013)

With the expansion of the use of reconfigurable logic circuits beyond commercial markets to avionic and military applications, designs in FPGA takes on the additional aspects of safety and national security. JTAG is a well-known standard mechanism in reconfigurable devices by allowing in-system design updates and debugging. Although it provides high controllability and observability, it also poses grave security challenges because of its read back and reprogramability features. The designer needs an effective tamper resistance mechanism to protect the intellectual property and sensitive data that might exist in a JTAG compliant FPGA based hardware system. In this paper, the main post-configuration vulnerabilities of FPGAs through JTAG are identified and preventive obfuscation models to guarantee secure platforms are proposed. The proposed obfuscation circuitry provides robust security features to overcome and prevent reverse engineering and unauthorized operation of the JTAG port, while occupying almost zero overhead.
Analogues of chloramphenicol. Part III (1954)

D. D. Evans, D. S. Morris, S. D. Smith and D. J. Tivey, J. Chem. Soc., 1954, 1687 DOI: 10.1039/JR9540001687
Antigenic and Genetic Variability of Human Metapneumoviruses (2004)

Human metapneumovirus (HMPV) is a member of the subfamily Pneumovirinae within the family Paramyxo- viridae. Other members of this subfamily, respiratory syncytial virus and avian pneumovirus, can be divided into subgroups on the basis of genetic or antigenic differences or both. For HMPV, the existence of different genetic lineages has been described on the basis of variation in a limited set of available sequences. We address the antigenic relationship between genetic lineages in virus neutralization assays. In addition, we analyzed the genetic diversity of HMPV by phylogenetic analysis of sequences obtained for part of the fusion protein (n = 84) and the complete attachment protein open reading frames (n = 35). On the basis of sequence diversity between attachment protein genes and the differences in virus neutralization titers, two HMPV serotypes were defined. Each serotype could be divided into two genetic lineages, but these did not reflect major antigenic differences.
Inhibition of pregnancy viability in mice following IL-2 administration. (1989)

The influence of administration of interleukin-2 (IL-2) on syngeneic and allogeneic murine pregnancy has been investigated. Human or mouse recombinant IL-2 (rhIL-2 and rmIL-2), or partially purified rat IL-2, was inoculated i.p. into C57B1 mice following syngeneic mating but before embryo implantation. This inhibited subsequent fetal development in up to 100% of cases, compared with mice inoculated with control material, including recombinant human interleukin-1 alpha (IL-1 alpha), where no inhibition of pregnancy viability was observed. Similar data were obtained in both syngeneic and allogeneic matings when rhIL-2 was administered on Day 1 of pregnancy. Administration of rhIL-2 during the second pregnancy, rather than a first pregnancy, was less effective. Administration of rhIL-2 during the first pregnancy does not induce a permanent sterility. Histological examination of the endometrium further demonstrated that mice injected with rhIL-2 on Day 1 of their first pregnancy showed a complete absence of embryonic tissue.
Matrix metalloproteinases and tissue inhibitors of metalloproteinases in human gliomas (1995)

The gene expression of five matrix metalloproteinases (MMPs) and two tissue inhibitors of metalloproteinases (TIMPs) was studied in human gliomas in vivo and in vitro to evaluate their roles in glioma invasion. Simultaneous expression of one to four MMP genes and two TIMP genes was found in 17 surgical glioma specimens, and one MMP (gelatinase A) gene and two TIMP genes were simultaneously expressed in tissue of three brains. The concomitant overexpression of gelatinase A, gelatinase B, and occasional matrilysin genes was associated with the malignancy of gliomas and accompanied by overexpression of the TIMP-1 gene. In five human glioma cell lines, gelatinase A, TIMP-1, and TIMP-2 genes were constitutively expressed in alll cell lines: the matrilysin gene in three cell lines; the stromelysin gene in two cell lines; and the interstitial collagenase gene in one cell line. There was a clear difference in the expression of gelatinase B and stromelysin genes between surgical glioma specimens and glioma cell lines: the gelatinase B gene was not expressed constitutively in vitro but was overexpressed in vivo, whereas the stromelysin gene was not expressed in vivo but was expressed in some cell lines. To find the cause of that difference in vivo and in vitro, the transcriptional regulations of MMP and TIMP genes by tumor promoter, growth factors, or cytokines were studied in vitro. Interstitial collagenase, gelatinase B, stromelysin, and TIMP-1 genes were upregulated in many cell lines by phorbol-12-myristate-13-acetate (PMA) and in some cell lines by epidermal growth factor, tumor necrosis factor-alpha, or interleukin-1 beta. Transforming growth factor-beta 1 (TGF beta 1) upregulated gelatinase A and matrilysin genes in some cell lines, and there were no clear responses from any MMP and TIMP genes to interleukin-6. Thus, the transcriptional modulation of MMP genes by these growth factors and cytokines seemed insufficient to explain the difference in gelatinase B and stromelysin gene expressions in vivo and in vitro and was suggestive of the genetic alteration of glioma cells in vitro, the heterogeneous cell population in glioma tissues, or both. Furthermore, the in vitro invasion of glioma cells through Matrigel in response to PMA, TGF beta 1, or TIMP-1 was assessed by chemoinvasion assay. In most cell lines, invasion was significantly stimulated by PMA or TGF beta 1 but suppressed by TIMP-1.(ABSTRACT TRUNCATED AT 400 WORDS)
Identification of human melanoma antigens recognized by T cells and their use for immuno-gene therapy. (1997)

Human malanoma antigens and their epitopes recognized by T cells have been identified using a variety of methods. These antigens are classified as 1) melanocyte specific melanosomal proteins (MART-1, gp100, tyrosinase, TRP-1 and TRP-2), 2) proteins expressed in testis and a variety of cancers (MAGE-1, MAGE-3, BAGE and GAGE), 3) tumor specific mutated proteins (-catenin, MUM-1 and CDK4), and 4)
Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers. (1998)

Direct DNA sequencing of human immunodeficiency virus type 1 (HIV-1) pol and env gene regions was characterized for accuracy and precision. Restricted maximum likelihood (REML) analysis of molecular clone reconstruction experiments using a primer-walking strategy showed that the BODIPY and BODIPY energy-transfer (BET) dye primers sets were significantly more accurate in quantitating heterogenous base mixtures than the fluorescein/rhodamine dye primers. Of the three sets examined, the BET dye primers were the most accurate. The improved accuracy correlated with the reduced emission band-widths of BODIPY and BET dye primers and the more uniform signal intensities of BET dye primers. However, comparing % coefficients of variation (CV) for the three dye primer sets, revealed that BODIPY dye primers gave better precision than both BET and fluorescein/rhodamine dye primer sets. Several sequence-dependent motifs were identified that showed specific nucleotide-biased incorporation and were determined to be the major variable component of the total %CV. Taken together, these results show that BODIPY and BET direct DNA sequencing can accurately and precisely characterize complex mixed-base populations.
The serum protein α2–Heremans-Schmid glycoprotein/fetuin-A is a systemically acting inhibitor of ectopic calcification (2003)

Ectopic calcification is a frequent complication of many degenerative diseases. Here we identify the serum protein alpha2-Heremans-Schmid glycoprotein (Ahsg, also known as fetuin-A) as an important inhibitor of ectopic calcification acting on the systemic level. Ahsg-deficient mice are phenotypically normal, but develop severe calcification of various organs on a mineral and vitamin D-rich diet and on a normal diet when the deficiency is combined with a DBA/2 genetic background. This phenotype is not associated with apparent changes in calcium and phosphate homeostasis, but with a decreased inhibitory activity of the Ahsg-deficient extracellular fluid on mineral formation. The same underlying principle may contribute to many calcifying disorders including calciphylaxis, a syndrome of severe systemic calcification in patients with chronic renal failure. Taken together, our data demonstrate a critical role of Ahsg as an inhibitor of unwanted mineralization and provide a novel therapeutic concept to prevent ectopic calcification accompanying various diseases.
Ultimate low loss of hollow-core photonic crystal fibres (2005)

Hollow-core photonic crystal fibres have excited interest as potential ultra-low loss telecommunications fibres because light propagates mainly in air instead of solid glass. We propose that the ultimate limit to the attenuation of such fibres is determined by surface roughness due to frozenin capillary waves. This is confirmed by measurements of the surface roughness in a HC-PCF, the angular distribution of the power scattered out of the core, and the wavelength dependence of the minimum loss of fibres drawn to different scales.
Distinct Mechanisms for K+ Efflux, Intoxication, and Hemolysis by Bordetella pertussis AC Toxin (1998)

Adenylate cyclase (AC) toxin from Bordetella pertussis delivers its catalytic domain to the interior of target cells where it converts host ATP to cAMP in a process referred to as intoxication. This toxin also hemolyzes sheep erythrocytes by a mechanism presumed to include pore formation and osmotic lysis. Intoxication and hemolysis appear at strikingly different toxin concentrations and evolve over different time scales, suggesting that different molecular processes may be involved. The present study was designed to test the hypothesis that intoxication and hemolysis occur by distinct mechanisms. Although the hemolytic activity of AC toxin has a lag of >1 h, intoxication starts immediately. Because of this difference, we sought a surrogate or precursor lesion that leads to hemolysis, and potassium efflux has been observed from erythrocytes treated with other pore-forming toxins. AC toxin elicits an increase in K+ efflux from sheep erythrocytes and Jurkat cells, a human T-cell leukemia line, that begins within minutes of toxin addition. The toxin concentration dependence along with the analysis of the time course suggest that toxin monomers are sufficient to elicit release of K+ and to deliver the catalytic domain to the cell interior. Hemolysis, on the other hand, is a highly cooperative event that likely requires a subsequent oligomerization of these individual units. Although induction of K+ efflux shares some structural and environmental requirements with both intoxication and hemolysis, it can occur under conditions in which intoxication is reduced or prevented. The data presented here suggest that the transmembrane pathway by which K+ is released is separate and distinct from the structure required for intoxication but may be related to, or a precursor of, that which is ultimately responsible for hemolysis.
Xenobiotic efflux pumps in isolated fish brain capillaries (2002)

To identify specific transporters that drive xenobiotics from the central nervous system to blood, the accumulation of fluorescent drugs was studied in isolated capillaries from killifish and dogfish shark brain using confocal microscopy and quantitative image analysis. In killifish brain capillaries, luminal accumulation of fluorescent derivatives of cyclosporin A and verapamil was concentrative, specific, and energy dependent (inhibition by KCN). Transport was reduced by PSC-833, but not by leukotriene C4, indicating the involvement of P-glycoprotein. The ability of capillaries to transport the cyclosporin A derivative was unchanged over 20 h, demonstrating the long-term viability of the preparation. Luminal accumulation of the fluorescent organic anions sulforhodamine 101 and fluorescein-methotrexate was also concentrative, specific, and energy dependent. Transport of these compounds was reduced by leukotriene C4, but not by PSC-833, indicating the involvement of a multidrug resistance-associated protein (Mrp). Similar results were obtained for isolated capillaries from dogfish shark. Immunostaining localized P-glycoprotein and Mrp2 to the luminal surface of the killifish brain capillary endothelium. These findings validate a new and long-lived comparative model for studying drug transport across the blood-brain barrier and, as in mammals, implicate P-glycoprotein and Mrp2 in transport from the central nervous system to blood in fish.
Exploring the Influence of National Cultures on Non-Compliance Behavior (2014)

IT organizations and CEO’s are, and should be, worried these days about the (lack of) data confidentiality and the usage of “shadow” IT systems by employees. In addition to the company’s risk of monetary loss or public embarrassment, the senior management themselves increasingly risk personal fines or even imprisonment. Several trends reinforce the attention for these subjects, including the fact that an increasing number of employees perform parts of their work tasks from home (RSA, 2007) and the increasing bandwidth available to users which makes them rely on the Internet for satisfying their business and personal computing needs (Desisto, Plummer, & Smith, 2008). Employees’ complying with the existing IT security policies is therefore essential. This paper presents a study on one of the factors that influence non-compliance behavior of insiders or employees in organizations: National Culture. The expected influence derived from researching literature has been tested in a survey study amongst employees of a big-5 accountancy firm in the Netherlands and Belgium. The study concludes that cultural aspects are indeed important factors influencing non-compliance behavior, but that not all expectations were confirmed.
Case Study: Minimization of Corrosion Using Activated Sodium Bromide in a Medium-Size Cooling Tower (1996)

Abstract The process loop cooling tower at the Albemarle Process Development Center in Baton Rouge, LA has historically used chlorine as the biocide together with industry accepted phosphorus-based corrosion/ scale inhibitors. Although this regimen provided biocontrol, sludge and iron build-up was a recurring problem, especially in low-velocity, small cross-sectional areas of piping. A general clean-up of the system was performed in April, 1995. This clean-up was followed with a switch to a two-component corrosion inhibitor/ dispersant package. It was decided to study alternate biocides as well at this time. Activated sodium bromide was found to be particularly effective in this tower, which operates at pH ~8.4. Relative to chlorine, the use of activated sodium bromide led to a decrease in general and pitting corrosion on mild steel while maintaining prior performance on admiralty brass. The reduced corrosion appears to be due to a combination of both chemical (less attack on passivated metal surfaces) and biological factors (better control of heterotrophic and sessile bacteria). These conclusions are supported by chemical analyses, corrosion meter and coupon data, dip slides, BART (biological activity reaction test) tests, and visual observations of the tower sump and heat exchanger surfaces.
CCR2 antagonism leads to marked reduction in proteinuria and glomerular injury in murine models of focal segmental glomerulosclerosis (FSGS) (2018)

Focal segmental glomerulosclerosis (FSGS) comprises a group of uncommon disorders that present with marked proteinuria, nephrotic syndrome, progressive renal failure and characteristic glomerular lesions on histopathology. The current standard of care for patients with FSGS include immunosuppressive drugs such as glucocorticoids followed by calcineurin inhibitors, if needed for intolerance or inadequate response to glucocorticoids. Renin-angiotensin-aldosterone (RAAS) blockers are also used to control proteinuria, an important signature of FSGS. Existing treatments, however, achieved only limited success. Despite best care, treatment failure is common and FSGS is causal in a significant proportion of end stage renal disease. Thus, an unmet need exists for novel disease modifying treatments for FSGS. We employed two widely-used murine models of FSGS to test the hypothesis that systemic inhibition of chemokine receptor CCR2 would have therapeutic benefit. Here we report that administration CCX872, a potent and selective small molecule antagonist of CCR2, achieved rapid and sustained attenuation of renal damage as determined by urine albumin excretion and improved histopathological outcome. Therapeutic benefit was present when CCX872 was used as a single therapy, and moreover, the combination of CCX872 and RAAS blockade was statistically more effective than RAAS blockade alone. In addition, the combination of CCR2 and RAAS blockade was equally as effective as endothelin receptor inhibition. We conclude that specific inhibition of CCR2 is effective in the Adriamycin-induced and 5/6 nephrectomy murine models of FSGS, and thus holds promise as a mechanistically distinct therapeutic addition to the treatment of human FSGS.
Passive Position Location Estimation Using the Extended Kalman Filter (1987)

Several papers have been published recently using the method ofleast squares for passive position location estimation. While the Kalman filter is mentioned as an alternative approach in most ofthese papers, none of the papers actually compare the performanceof the Kalman filter with the method of least squares. In this paper,the performances of the extended Kalman filter and the iteratedextended Kalman filter are compared with the method of leastsquares. Monte Carlo results are given showing how the a prioricovariance matrix influences the accuracy of the extended Kalmanfilter.
The influence of the surgical wound on local tumor recurrence. (1989)

Failure of a primary surgical treatment for cancer is often caused by recurrence of the tumor at the surgical site. The KHT mouse tumor system recapitulates this experience and provides a useful model to test strategies for reducing the incidence of local recurrence after surgical excision. There was an 82% local recurrence of the KHT tumor after surgery. A cell dilution assay indicated that it would require only 39 tumor cells injected into the wound site to result in the same (82%) incidence of tumors. This figure is in contrast to 340 cells required when the cells were injected into an unwounded flank. With the B16 melanoma in C57B1 mice and the Meth A sarcoma in BALB/c mice, the number of cells necessary to induce a tumor (TD/50) was also significantly reduced when the cells were injected into a surgical wound rather than into nonwounded tissue. The difference in cell number was interpreted as the result of the presence of growth factors derived from the traumatized tissue and the inflammatory cells at the wound site. Neither a 5 nor a 15 Gy dose of x-radiation delivered to the wound site immediately after surgical excision of the KHT tumor resulted in a significant reduction in the incidence of local recurrences. When the same doses of x-radiation were given immediately after injecting 36 KHT cells into a wound, no tumors developed. This difference was believed to have resulted from the hypoxic condition in the wound site and the presence of residual clonogenic tumor cells in a nonproliferating (radioresistant) state.
Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome (2015)

With the expanding interest in RNA biology, interest in artificial RNA-binding proteins (RBPs) is likewise increasing. RBPs can be designed in a modular fashion, whereby effector and RNA-binding domains are combined in chimeric proteins that exhibit both functions and can be applied for regulation of a broad range of biological processes. The elucidation of the RNA recognition code for Pumilio and fem-3 mRNA-binding factor (PUF) homology proteins allowed engineering of artificial RBPs for targeting endogenous mRNAs. In this review, we will focus on the recent advances in elucidating and reprogramming PUF domain specificity, update on several promising applications of PUF-based designer RBPs, and discuss some other domains that hold the potential to be used as the RNA-binding scaffolds for designer RBP engineering.