gebhart/patrepeval huggingface dataset:
The MUR1 gene of Arabidopsis thaliana encodes an isoform of GDP- d -mannose-4,6-dehydratase, catalyzing the first step in the de novo synthesis of GDP- l -fucose (1997)

GDP-L-fucose is the activated nucleotide sugar form of L-fucose, which is a constituent of many structural polysaccharides and glycoproteins in various organisms. The de novo synthesis of GDP-L-fucose from GDP-D-mannose encompasses three catalytic steps, a 4,6-dehydration, a 3,5-epimerization, and a 4-reduction. The mur1 mutant of Arabidopsis is deficient in L-fucose in the shoot and is rescued by growth in the presence of exogenously supplied L-fucose. Biochemical assays of the de novo pathway for the synthesis of GDP-L-fucose indicated that mur1 was blocked in the first nucleotide sugar interconversion step, a GDP-D-mannose-4,6-dehydratase. An expressed sequence tag was identified that showed significant sequence similarity to proposed bacterial GDP-D-mannose-4,6-dehydratases and was tightly linked to the mur1 locus. A full-length clone was isolated from a cDNA library, and its coding region was expressed in Escherichia coli. The recombinant protein exhibited GDP-D-mannose-4,6-dehydratase activity in vitro and was able to complement mur1 extracts in vitro to complete the pathway for the synthesis of GDP-L-fucose. All seven mur1 alleles investigated showed single point mutations in the coding region for the 4,6-dehydratase, confirming that it represents the MUR1 gene.
Low Levels of Endogenous Androgens Increase the Risk of Atherosclerosis in Elderly Men: The Rotterdam Study (2002)

In both men and women, circulating androgen levels decline with advancing age. Until now, results of several small studies on the relationship between endogenous androgen levels and atherosclerosis have been inconsistent. In the population-based Rotterdam Study, we investigated the association of levels of dehydroepiandrosterone sulfate (DHEAS) and total and bioavailable testosterone with aortic atherosclerosis among 1,032 nonsmoking men and women aged 55 yr and over. Aortic atherosclerosis was assessed by radiographic detection of calcified deposits in the abdominal aorta, which have been shown to reflect intimal atherosclerosis. Relative to men with levels of total and bioavailable testosterone in the lowest tertile, men with levels of these hormones in the highest tertile had age-adjusted relative risks of 0.4 [95% confidence interval (CI), 0.2-0.9] and 0.2 (CI, 0.1-0.7), respectively, for the presence of severe aortic atherosclerosis. The corresponding relative risks for women were 3.7 (CI, 1.2-11.6) and 2.3 (CI, 0.7-7.8). Additional adjustment for cardiovascular disease risk factors did not materially affect the results in men, whereas in women the associations diluted. Men with levels of total and bioavailable testosterone in subsequent tertiles were also protected against progression of aortic atherosclerosis measured after 6.5 yr (SD +/- 0.5 yr) of follow-up (P for trend = 0.02). No clear association between levels of DHEAS and presence of severe aortic atherosclerosis was found, either in men or in women. In men, a protective effect of higher levels of DHEAS against progression of aortic atherosclerosis was suggested, but the corresponding test for trend did not reach statistical significance. In conclusion, we found an independent inverse association between levels of testosterone and aortic atherosclerosis in men. In women, positive associations between levels of testosterone and aortic atherosclerosis were largely due to adverse cardiovascular disease risk factors.
Poly-N-acetyllactosaminyl O-glycans attached to leukosialin. The presence of sialyl Le(x) structures in O-glycans. (1992)

Poly-N-acetyllactosamine extension has been found in O-glycans in addition to N-glycans and glycosphingolipids. Attempts were made in HL-60 and K562 cells to determine the amount of poly-N-acetyllactosaminyl O-glycans in the major sialoglycoprotein, leukosialin. Leukosialin was immunoprecipitated from [3H]glucosamine-labeled HL-60 and K562 cells. Glycopeptides were prepared by Pronase digestion, and O-glycan-containing glycopeptides were isolated by affinity chromatography using Jacalin-agarose. The glycopeptides bound to Jacalin-agarose and those unbound were treated with alkaline borohydride, and the released O-glycans were fractionated by Bio-Gel P-4 filtration. Sequential glycosidase digestion of the O-glycans, with or without pretreatment by fucosidase or neuraminidase, revealed the following conclusions. 1) Leukosialin from HL-60 cells contains about 1-2 poly-N-acetyllactosaminyl O-glycan chains/molecule. 2) About 50% of these poly-N-acetyllactosaminyl O-glycans contain sialyl Le(x) termini, NeuNAc alpha 2-->3Gal beta 1-->4 (Fuc alpha 1-->3)GlcNAc beta 1-->R. The amount of sialyl Le(x) structure in leukosialin is roughly equivalent to that on cell surfaces of HL-60 cells. 3) Leukosialin from K562 cells, on the other hand, contains no detectable amount of poly-N-acetyllactosaminyl O-glycans. 4) The presence of poly-N-acetyllactosamine in O-glycans is dependent on the core 2 beta 1,6-N-acetylglucosaminyl transferase. 5) Jacalin-agarose binds to sialylated small oligosaccharides such as NeuNAc alpha 2-->3Gal beta 1-->3(NeuNAc alpha 2-->6) GalNAc but not the hexasaccharide NeuNAc alpha 2-->3Gal beta 1-->3(NeuNAc alpha 2-->3Gal beta 1-->4GlcNAc beta 1-->6) GalNAc. These results indicate that the formation of polylactosaminyl O-glycans and sialyl Le(x) structure in O-glycans is dependent on the core 2 formation.
Back Driving Assistant for Passenger Cars with Trailer (2006)

&lt;div class="htmlview paragraph"&gt;This paper focuses on control strategies that are needed to stabilise a backing trailer and steer it into the desired direction. A model of the trailer and the car is used in order to calculate the desired steering wheel angle. An important constraint is that the driver should not be disturbed by the steering intervention. Measurements are done with a prototype car with an active front steering system. The results show that the drivers manage to fulfill the given driving task faster and with less steering wheel activity than without the assistant.&lt;/div&gt;
Extending lifetime of flash memory using strong error correction coding (2015)

Demand for flash memory based storage systems is on the rise because flash memory has many advantages when compared with hard disk drives, such as lower latency and resistance to physical shock. However, flash memory permits only a limited number of program/erase (P/E) cycles, and after the guaranteed number of P/E cycles, data cannot be reliably retrieved due to uncorrectable errors. Given a target bit error rate, the guaranteed number of P/E cycles decreases as more bits are stored in one cell and as the cell size is scaled down. In this paper, a novel lifetime extension mechanism for flash memory, referred to as a gradual error correction code (GECC), is proposed. A G-ECC provides a stronger level of error correction than a standard ECC by sacrificing a small portion of storage capacity in order to store additional parity bits. The proposed method can extend the lifetime of flash memory by 124% at the cost of a 12% loss in capacity. The use of additional parity bits necessarily leads to performance loss due to increased accesses for those additional parity bits and garbage collection operations involving those bits. Thus, methods to alleviate such performance loss are proposed; these methods reduce the performance overhead from 17% (without the proposed methods) to 3% even in the worst case.
Nucleotide Analogs: Synthesis and Biological Function (1980)

First comprehensive introduction to application of nucleotide analogs in study of biological systems. Describes present knowledge of synthesis, chemistry, biochemistry, and applications. Particular attention given to those that contribute to understanding of structure-function relationships. Subject presented in illustrative, textbook manner; chemical structural formulas and reaction schemes are employed wherever possible.
Optimal fuzzy controller in the carbonization control system at the soda production (2019)

Предметом дослідження в даній статті є процедура синтезу нечіткого контролера в системі управління відділенням карбонізації у виробництві кальцинованої соди. Метою роботи є розробка оптимального нечіткого контролеру, використання якого в системі управління зумовлювало оптимальний результат згідно встановленим критеріям. Завдання. На основі існуючих підходів до синтезу нечіткого контролеру розробити процедуру синтезу оптимального нечіткого ПІД контролеру (НПІДК) відповідно до цілей управління. Процедура побудови контролера залежить як від структури контролера, так і від параметрів нечіткого налаштування, таких як кількість функції приналежності, їх вигляд, параметри, що визначають функцію приналежності. В результаті проведеного моделювання системи управління відділенням карбонізації було показано залежність кінцевого результату від параметрів нечіткого налаштування. Висновки. На підставі запропонованих методів синтезу розроблено структури оптимальних НПІДК з різними наборами параметрів нечіткого налаштування. Показано, що будь який оптимальний нечіткий ПІД регулятор дає кращі показники, ніж класичний контролер, та найкращим з них є регулятор,в якому&#13;\nблок нечіткого налаштування має гаусові функції приналежності.
Optical Manipulation with Plasmonic Beam Shaping Antenna Structures (2012)

Near-field optical trapping of objects using plasmonic antenna structures has recently attracted great attention. However, metal nanostructures also provide a compact platform for general wavefront engineering of intermediate and far-field beams. Here, we analyze optical forces generated by plasmonic beam shaping antenna structures and show that they can be used for general optical manipulation such as guiding of a dielectric particle along a linear or curved trajectory. This removes the need for bulky diffractive optical components and facilitates the integration of optical force manipulation into a highly functional, compact system.
Specific cellular immune response and neutralizing antibodies in goats immunized with native or recombinant envelope proteins derived from human T-lymphotropic virus type IIIB and in human immunodeficiency virus-infected men. (1987)

Animals immunized with native or recombinant envelope proteins from the human immunodeficiency virus (HIV, formerly referred to as human T-lymphotropic virus type III) human T-lymphotropic virus type IIIB and naturally HIV-infected men were assessed for neutralizing antibodies and cell-mediated immunity toward the virus. Immunization of rabbits or goats with the native external envelope glycoprotein gp120 or with corresponding recombinant proteins elicited strictly type-specific neutralizing antibodies. A broad, group-specific cellular immune response to gp120 and to three different HIV isolates was seen in goats immunized with the native gp120 but not in animals immunized with the nonglycosylated recombinant envelope proteins. In HIV-infected people, no T-cell response was seen, even though their T-cell response toward other foreign antigens was intact. The results show type- and group-specific epitopes on gp120, some of which may be of importance for the development of a vaccine against HIV infection.
Insertion Sequences (1998)

Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available.
Robust Techniques for Computer Vision (2004)

ysis 1995, pages 191--208. AddisonWesley Longman, 1996. [116] R. H. Zamar. Robust estimation in the errors-in-variables model. Biometrika, 76:149-- 160, 1989. [117] Z. Zhang. Determining the epipolar geometry and its uncertainty: A review. Intl. J. of Computer Vision, 27:161--195, 1998. [118] Z.Y. Zhang. Parameter-estimation techniques: A tutorial with application to conic fitting. Image and Vision Computing, 15:59--76, 1997. [89] P. J. Rousseeuw and C. Croux. Alternatives to the median absolute deviation. J. of Amer. Stat. Assoc., 88:1273--1283, 1993. [90] P. J. Rousseeuw and A. M. Leroy. Robust Regression and Outlier Detection. Wiley, 1987. [91] D. Ruppert and D. G. Simpson. Comment on &amp;quot;Unmasking Multivariate Outliers and Leverage Points&amp;quot;, by P. J. Rousseeuw and B. C. van Zomeren. J. of Amer. Stat. Assoc., 85:644--646, 1990. [92] D. W. Scott. Parametric statistical modeling by minimum integrated square error. Technometrics, 43:247--285, 2001. [93] B. W. Silverman. Density Est
Mitogenesis and protein synthesis: A role for ribosomal protein S6 phosphorylation? (1994)

It has been known for 20 years that the ribosomal protein S6 is rapidly phosphorylated when cells are stimulated to grow or divide. Furthermore, numerous studies have documented that there is a strong correlation between increases in S6 phosphorylation and protein synthesis, leading to the idea that S6 phosphorylation is involved in up-regulating translation. In an attempt to define a mechanism by which S6 phosphorylation exerts translational control, other studies have focused on characterizing the sites of phosphorylation of this protein and its location within the ribosome. Recent data show that S6 is a protein which may have diverse cellular functions and is essential for normal development, and that it may be involved in the translational regulation of a specific class of messages.
Thalidomide selectively inhibits tumor necrosis factor alpha production by stimulated human monocytes. (1991)

Thalidomide selectively inhibits the production of human monocyte tumor necrosis factor alpha (TNF-alpha) when these cells are triggered with lipopolysaccharide and other agonists in culture. 40% inhibition occurs at the clinically achievable dose of the drug of 1 micrograms/ml. In contrast, the amount of total protein and individual proteins labeled with [35S]methionine and expressed on SDS-PAGE are not influenced. The amounts of interleukin 1 beta (IL-1 beta), IL-6, and granulocyte/macrophage colony-stimulating factor produced by monocytes remain unaltered. The selectivity of this drug may be useful in determining the role of TNF-alpha in vivo and modulating its toxic effects in a clinical setting.
Bifidobacterium brevereduces apoptotic epithelial cell shedding in an exopolysaccharide and MyD88-dependent manner (2017)

Certain members of the microbiota genus Bifidobacterium are known to positively influence host well-being. Importantly, reduced bifidobacterial levels are associated with inflammatory bowel disease (IBD) patients, who also have impaired epithelial barrier function, including elevated rates of apoptotic extrusion of small intestinal epithelial cells (IECs) from villi-a process termed 'cell shedding'. Using a mouse model of pathological cell shedding, we show that mice receiving Bifidobacterium breve UCC2003 exhibit significantly reduced rates of small IEC shedding. Bifidobacterial-induced protection appears to be mediated by a specific bifidobacterial surface exopolysaccharide and interactions with host MyD88 resulting in downregulation of intrinsic and extrinsic apoptotic responses to protect epithelial cells under highly inflammatory conditions. Our results reveal an important and previously undescribed role for B. breve, in positively modulating epithelial cell shedding outcomes via bacterial- and host-dependent factors, supporting the notion that manipulation of the microbiota affects intestinal disease outcomes.
Iso-Shaping Rigid Bodies for Estimating Their Motion From Image Sequences (2004)

In many medical imaging applications, due to the limited field of view of imaging devices, acquired images often include only a part of a structure. In such situations, it is impossible to guarantee that the images will contain exactly the same physical extent of the structure at different scans, which leads to difficulties in registration and in many other tasks, such as the analysis of the morphology, architecture, and kinematics of the structures. To facilitate such analysis, we developed a general method, referred to as iso-shaping, that generates structures of the same shape from segmented image sequences. The basis for this method is to automatically find a set of key points, called shape centers, in the segmented partial anatomic structure such that these points are present in all images and that they represent the same physical location in the object, and then trim the structure using these points as reference. The application area considered here is the analysis of the morphology, architecture, and kinematics of the joints of the foot from magnetic resonance images acquired at different joint positions and load conditions. The accuracy of the method is analyzed by utilizing ten data sets for iso-shaping the tibia and the fibula via four evaluative experiments. The analysis indicates that iso-shaping produces results as predicted by the theoretical framework.
Ligands for the receptor tyrosine kinases hek and elk: isolation of cDNAs encoding a family of proteins. (1995)

Hek is a member of the eph subfamily of receptor tyrosine kinases whose members include elk, hek2, sek, eph and eck among others. Using a soluble form of hek consisting of the extracellular region of the receptor fused to the Fc domain of human IgG1 and an expression cloning strategy, we have isolated two different but related cDNAs from the human T-lymphoma line HSB-2 that encode ligands for hek. The cDNAs encode proteins of 238 and 201 amino acids (44% amino acid identity) that are anchored to the membrane by glycosylphosphatidylinositol (GPI)-linkage. The proteins encoded by these cDNAs are bound by hek with affinity constants of 2 x 10(8) M-1. These proteins also bind the elk tyrosine kinase receptor. These cDNAs are related to other cDNAs that we have recently isolated from a human placental library that encode ligands for both hek and elk and define an emerging family of ligands for eph-related kinases (LERKs).
Regulation of Single-stranded DNA Binding by the C Termini of Escherichia coli Single-stranded DNA-binding (SSB) Protein (2010)

The homotetrameric Escherichia coli single-stranded DNA-binding (SSB) protein plays a central role in DNA replication, repair, and recombination. In addition to its essential activity of binding to transiently formed single-stranded (ss) DNA, SSB also binds an array of partner proteins and recruits them to their sites of action using its four intrinsically disordered C-terminal tails. Here we show that the binding of ssDNA to SSB is inhibited by the SSB C-terminal tails, specifically by the last 8 highly acidic amino acids that comprise the binding site for its multiple partner proteins. We examined the energetics of ssDNA binding to short oligodeoxynucleotides and find that at moderate salt concentration, removal of the acidic C-terminal ends increases the intrinsic affinity for ssDNA and enhances the negative cooperativity between ssDNA binding sites, indicating that the C termini exert an inhibitory effect on ssDNA binding. This inhibitory effect decreases as the salt concentration increases. Binding of ssDNA to approximately half of the SSB subunits relieves the inhibitory effect for all of the subunits. The inhibition by the C termini is due primarily to a less favorable entropy change upon ssDNA binding. These observations explain why ssDNA binding to SSB enhances the affinity of SSB for its partner proteins and suggest that the C termini of SSB may interact, at least transiently, with its ssDNA binding sites. This inhibition and its relief by ssDNA binding suggest a mechanism that enhances the ability of SSB to selectively recruit its partner proteins to sites on DNA.
Importance of Gonadal Steroids to Bone Mass in Men with Hyperprolactinemic Hypogonadism (1989)

The reversal of hypogonadism, independent of the prolactin concentration, is associated with an improvement in bone mass. Our findings emphasize the importance of gonadal steroids in maintaining skeletal integrity in men.
Role of a structural glycoprotein of pseudorabies in virus virulence (1987)

The virulence of deletion mutants of pseudorabies virus defective in the expression of glycoprotein gI, gp63, or both was tested in 1-day-old chickens and young pigs. In the absence of expression of gI, the virulence of a fully virulent laboratory strain, PrV(Ka), for 1-day-old chickens was reduced approximately fourfold. Inactivation of glycoprotein gp63 appeared also to affect the virulence of PrV(Ka) only slightly, as did inactivation of both gI and gp63. The level of reduction in virulence, however, was considerably more marked in Bartha 43/25aB4, a less virulent virus strain. Inactivation of the expression of gI in Bartha 43/25aB4 reduced virulence for chickens at least 100-fold. The results obtained when the virulence of the mutants for pigs was determined were compatible with those obtained for chickens. These results indicate that gI plays a role in virulence, but that it does so in conjunction with at least one other viral function (a function that is defective in Bartha 43/25aB4).