gebhart/patrepeval huggingface dataset:
Phase Behavior and Self-Assembly of Perfectly Sequence-Defined and Monodisperse Multiblock Copolypeptides (2017)

This paper investigates how the properties of multiblock copolypeptides can be tuned by their block architecture, defined by the size and distribution of blocks along the polymer chain. These parameters were explored by the precise, genetically encoded synthesis of recombinant elastin-like polypeptides (ELPs). A family of ELPs was synthesized in which the composition and length were conserved while the block length and distribution were varied, thus creating 11 ELPs with unique block architectures. To our knowledge, these polymers are unprecedented in their intricately and precisely varied architectures. ELPs exhibit lower critical solution temperature (LCST) behavior and micellar self-assembly, both of which impart easily measured physicochemical properties to the copolymers, providing insight into polymer hydrophobicity and self-assembly into higher order structures, as a function of solution temperature. Even subtle variation in block architecture changed the LCST phase behavior and morphology of these ELPs, measured by their temperature-triggered phase transition and nanoscale self-assembly. Size and morphology of polypeptide micelles could be tuned solely by controlling the block architecture, thus demonstrating that when sequence can be precisely controlled, nanoscale self-assembly of polypeptides can be modulated by block architecture.
A tumor necrosis factor-binding protein purified to homogeneity from human urine protects cells from tumor necrosis factor toxicity (1989)

Unfractionated preparations of the proteins of human urine provided protection against the in vitro cytocidal effect of tumor necrosis factor (TNF). In certain cells, the proteins decreased expression of the receptors for TNF in a temperature-dependent way. In all cells examined, the proteins were found to interfere also with the binding of both TNF and interleukin-1 when applied directly into the binding assays. That effect could be observed in the cold, suggesting that it was independent of cellular metabolism. A protein which protects cells against the cytotoxicity of TNF was purified from human urine by chromatography on CM-Sepharose followed by high performance liquid chromatography on Mono Q and Mono S columns and reversed phase high performance liquid chromatography. This protein is a very minor constituent of normal urine, with an apparent molecular weight of about 27,000 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis under both reducing and nonreducing conditions. Homogeneity of the purified protein was confirmed by microsequence analysis which revealed a single N-terminal sequence: Asp-Ser-Val-Cys-Pro-. The protein protected cells from TNF toxicity at concentrations of a few nanograms per ml and interfered with the binding of both TNF-alpha and TNF-beta to cells, when applied simultaneously with the cytokines. However, unlike crude preparations of the urinary proteins, the purified protein did not induce in cells a decrease in ability to bind TNF nor did it interfere with the binding of interleukin-1 to its receptor. Direct, specific binding to the protein of TNF-alpha and, to a lesser extent, also TNF-beta, but not of interleukin-1 nor interferon-gamma could be demonstrated. It is suggested that this protein blocks the function of TNF by competing for TNF with the TNF receptor and not by interacting with the target cell.
Production costs of liquid fuels from biomass (1994)

There has been considerable interest in producing fuels from biomass and wastes since the oil crises of the last two decades which has been reinforced by subsequent environmental concerns and recent political events in the Middle East. This project was undertaken to provide a consistent and thorough review of the full range of processes for producing liquid fuels from biomass to compare both alternative technologies and processes within those technologies in order to identify the most promising opportunities that deserve closer attention. Thermochemical conversion of wood, straw and refuse includes both indirect liquefaction through gasification, and direct liquefaction through pyrolysis and liquefaction in pressurised solvents. Biochemical conversion is based on a different set of feedstocks that includes wood as well as wheat and sugar beet. Both acid and enzyme hydrolysis are included as options, followed by fermentation. The liquid products considered include gasoline and diesel hydrocarbons that would in some cases would require minor refining to convert them into marketable products, and conventional alcohol fuels of methanol and ethanol which have established opportunities for utilisation, and fuel alcohol which is as yet unproven in the market place. Results are given both as absolute fuel costs and as a comparison of estimated cost to market price. The results from these two interpretations are quite different. In terms of absolute fuel costs, thermochemical conversion offers the lowest cost products, with the least complex processes generally having an advantage. Exceptions are the unproven direct liquefaction route through zeolites which may be very optimistic, and the Shell SMDS process. Biochemical routes are the least attractive. The most attractive processes from comparing production costs to product values are generally the alcohol fuels which enjoy a higher market value. This final analysis should be viewed cautiously since product values are very uncertain and can change significantly over short periods of time, and feedstock prices are also subject to substantial variation with time and location, and this is often the major cost item in the production costs. There is still considerable analysis to be carried out on results from the model, including production cost analyses and sensitivity studies, as well as continued development to improve accuracy and extend the range of technologies considered.
The influence of temperature on the tension developed in an isometric twitch (1951)

Abstract In muscular contraction the development of tension requires that the contractile component should shorten and stretch the series elastic component. In an isometric twitch the maximum tension is reached as a balance between two opposing processes, internal shortening on the one hand and decay of the active state (relaxation) on the other. The fact that the maximum tension in a twitch is considerably less than in a tetanus has been attributed to oncoming relaxation allowing insufficient time for internal shortening to be completed. The maximum tension in a twitch is considerably reduced by a rise of temperature, while that in a tetanus is somewhat increased. This would require that the temperature coefficient of the velocity of shortening should be substantially less than that of the decay of activity. Evidence for this exists. On this view the effect of a quick stretch, applied during the early stage of a twitch, in increasing the tension ratio, stretch/isometric, should be much greater at a higher temperature. This expectation is confirmed on frogs’ muscles over the range 0 to 20°C. The effect of temperature, therefore, on the size of a twitch can be attributed to the difference between the temperature coefficients of velocity of shortening and rate of relaxation.
Receptor for interleukin 13 is a marker and therapeutic target for human high-grade gliomas. (1999)

Glioblastoma multiforme (GBM) is an incurable brain tumor. Due to the striking heterogeneity that characterizes GBM, there is no known tumor-specific antigen or receptor that is expressed by a majority of GBM patients. We found that virtually all studied human GBM specimens (23 samples) abundantly expressed a receptor for interleukin (IL)-13 in situ, whereas normal human brain had few, if any, IL-13-binding sites. The GBM-associated IL-13 receptor was both quantitatively and qualitatively different from and, thus, more restrictive than the shared signaling receptor of normal tissue: it was IL-4 independent. The receptor for IL-13 was overexpressed by a majority of cancer cells in situ. Furthermore, cytotoxins targeted to this more restrictive IL-13R produced cures in animals bearing xenografts of human high-grade gliomas. Thus, unexpectedly, the receptor for an immune regulatory cytokine may be a long sought marker and, concomitantly, a unique imaging site and therapeutic target for GBM, the most malignant and the most heterogeneous of brain tumors.
An efficient block-matching algorithm for motion-compensated coding (2005)

We present an efficient search technique which minimizes the computations necessary for estimating the motion in video-sequences by the block matching method. We also discuss the theoretical basis for conducting such a reduced search by our technique. We then present two algorithms which employ the proposed technique for estimating the motion typical of video-conferencing environment. Next, the results of computer simulations on a real video-sequence are included which demonstrate the effectiveness of the proposed technique. Finally, the results of a study of statistical properties of block motion-compensated frame difference signals are also summarized, to assist in future choice of a coding strategy for such signals.
[Efficiency of control of Ixodes ticks, vectors of natural and focal infections in the south of the Tyumen Region]. (2005)

There are synchronous undulating variations in the number of ticks and in the incidence of tick-borne encephalitis and Ixodes tick-borne borreliosis in the south of the Tyumen Region. Since 1990s, there has been an increase in the incidence of tick-borne infections and in the number of ticks. The highest epidemic risk areas of 1418 have been treated with acaricides due to the additional financing made by the Tyumen Region in 2002-2004. The treatments with the agents Sipaz-super and Briz (25% c.e. cipermethrin) have ensured 98-100% freedom of the areas from ticks. In Tyumen and in the south of the Tyumen Region, the number of human suction of ticks has reduced from 601 and 1231 per 100,000 in 2001 to 424 and 658 cases in 2004, respectively. The authors have developed guidelines for tick-controlling measures in large areas of the Tyumen Region.
Dynamic modeling of robotic fish and its experimental validation (2011)

In this paper, we present a new dynamic model for a carangiform robotic fish by merging rigid-body dynamics with Lighthill's large-amplitude elongated-body theory. In addition, we refine the model by introducing an effective approach to the evaluation of time-varying drag force and moment coefficients. It is known that these coefficients vary with the angle of attack, but the angle of attack oscillates constantly for a carangiform robotic fish because of the recoil motion of the body. By examining the individual effects of tail beat bias, frequency, amplitude on the attack angle, we find that the bias has much more dominant impact than the other two factors. Based on this observation, we develop a convenient scheme for determining the drag force and moment coefficients, as a function of the tail beat bias. Experimental results on a robotic fish prototype propelled with a servo-controlled rigid tail have verified the proposed model. In particular, we show that the pressure force at the tail tip, which is often ignored in related literature, plays a significant role in the dynamics. The effectiveness of the proposed scheme for adapting the drag force and moment coefficients is also demonstrated through the comparison with a model that uses constant drag coefficients.
Structural and Functional Characterization of Gene Clusters Directing Nonribosomal Synthesis of Bioactive Cyclic Lipopeptides in Bacillus amyloliquefaciens Strain FZB42 (2004)

The environmental strain Bacillus amyloliquefaciens FZB42 promotes plant growth and suppresses plant pathogenic organisms present in the rhizosphere. We sampled sequenced the genome of FZB42 and identified 2,947 genes with >50% identity on the amino acid level to the corresponding genes of Bacillus subtilis 168. Six large gene clusters encoding nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) occupied 7.5% of the whole genome. Two of the PKS and one of the NRPS encoding gene clusters were unique insertions in the FZB42 genome and are not present in B. subtilis 168. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis revealed expression of the antibiotic lipopeptide products surfactin, fengycin, and bacillomycin D. The fengycin (fen) and the surfactin (srf) operons were organized and located as in B. subtilis 168. A large 37.2-kb antibiotic DNA island containing the bmy gene cluster was attributed to the biosynthesis of bacillomycin D. The bmy island was found inserted close to the fen operon. The responsibility of the bmy, fen, and srf gene clusters for the production of the corresponding secondary metabolites was demonstrated by cassette mutagenesis, which led to the loss of the ability to produce these peptides. Although these single mutants still largely retained their ability to control fungal spread, a double mutant lacking both bacillomycin D and fengycin was heavily impaired in its ability to inhibit growth of phytopathogenic fungi, suggesting that both lipopeptides act in a synergistic manner.
A Comparison of the In Vitro Effects of 2’Fucosyllactose and Lactose on the Composition and Activity of Gut Microbiota from Infants and Toddlers (2021)

Because of the recognized health benefits of breast milk, it is recommended as the sole nutrition source during the first 6 months of life. Among the bioactive components are human milk oligosaccharides (HMOs) that exert part of their activity via the gut microbiota. Here, we investigated the gut microbiota fermentation of HMO 2'fucosyllactose (2'-FL), using two in vitro models (48 h fecal incubations and the long-term mucosal simulator of the human intestinal microbial ecosystem [M-SHIME<sup>®</sup>]) with fecal samples from 3-month-old breastfed (BF) infants as well as 2-3 year old toddlers. The short-term model allowed the screening of five donors for each group and provided supportive data for the M-SHIME<sup>®</sup> study. A key finding was the strong and immediate increase in the relative abundance of <i>Bifidobacteriaceae</i> following 2'-FL fermentation by both the BF infant and toddler microbiota in the M-SHIME<sup>®</sup>. At the metabolic level, while decreasing branched-chain fatty acids, 2'-FL strongly increased acetate production together with increases in the health-related propionate and butyrate whilst gas production only mildly increased. Notably, consistently lower gas production was observed with 2'-FL fermentation as compared to lactose, suggesting that reduced discomfort during the dynamic microbiome establishment in early life may be an advantage along with the bifidogenic effect observed.
The new kids on the block: ADAMTSs, potentially multifunctional metalloproteinases of the ADAM family (2000)

Cell-cell and cell-matrix interactions are of vital importance not only for proper cellular homeostasis during embryogenesis and development of an organism, but also in pathological states in diseases ranging from tumor metastasis to AIDS. Tissues owe their dynamic structure both to changes in expression of adhesive proteins and their receptors and to the regulated action of secreted proteinases, particularly members of the metalloproteinase family. Many of these secreted and cell surface proteins and metalloproteinases are found at critical locations that facilitate their involvement in cell-cell and cell-matrix interactions. Metalloproteinases belong to a superfamily of zinc-dependent proteases known as metzincins. Based on sequence and structural similarities, metzincins
Bone Graft For Revision Hip Arthroplasty (2003)

Revision total hip arthroplasty often presents surgeons with difficult bone loss problems. The selection of an appropriate bone graft is influenced by the size of the bone defect, the location, the biology of the bone graft site, and whether the graft is required for structural support. Autogenous bone graft remains the gold standard bone graft material but there only is a limited amount available and there is morbidity associated with the harvesting of these grafts. The most frequently used bone graft materials include autogenous iliac crest bone graft, cancellous allograft chips, demineralized bone matrix, and bulk structural allografts (femoral head, distal or proximal femoral allograft, whole acetabuli, and femoral strut grafts). It often is difficult to determine on plain radiographs whether nonstructural grafts actually incorporate into the host bone. Recently, attention has focused on the use of new materials for bone grafting including: new demineralized bone matrices, ceramics, autologous platelet concentrates, recombinant proteins, and stem cells. The purpose of this review was to assess the biologic potential of these nonstructural grafts in revision hip arthroplasty and their limitations. Are these agents actually incorporating into host bone? Future bone graft options, including tissue engineering and gene therapy will be discussed briefly.
Diffusion-Induced Imperfections in Silicon (1965)

Diffusion‐induced dislocations and precipitates have been studied through electron microscopy as a function of the diffusion depth. High concentrations of phosphorus and arsenic were diffused in (111) Si wafers to a shallow depth under the condition of constant solute surface concentration. Extensive dislocation networks were observed in phosphorus diffused wafers, whereas only a few single dislocations were detected in arsenic‐diffused wafers. The results are shown to be in general agreement with Prussin's model of dislocation generation by relief of the stress due to solute lattice contraction of P and As.
Polyploidy‐Associated Genomic Instability in Arabidopsis thaliana (2010)

Abstract Formation of polyploid organisms by fertilization of unreduced gametes in meiotic mutants is believed to be a common phenomenon in species evolution. However, not well understood is how species in nature generally exist as haploid and diploid organisms in a long evolutionary time while polyploidization must have repeatedly occurred via meiotic mutations. Here, we show that the ploidy increased for two consecutive generations due to unreduced but viable gametes in the Arabidopsis cyclin a1;2‐2 (also named tardy asynchronousmeiosis‐2) mutant, but the resultant octaploid plants produced progeny of either the same or reduced ploidy via genomic reductions during meiosis and pollen mitosis. Ploidy reductions through sexual reproduction were also observed in independently generated artificial octaploid and hexaploid Arabidopsis plants. These results demonstrate that octaploid is likely the maximal ploidy produced through sexual reproduction in Arabidopsis. The polyploidy‐associated genomic instability may be a general phenomenon that constrains ploidy levels in species evolution.
Human ovarian cancer xenografts in nude mice (1998)

The new cytostatics titanocene dichloride and vinorelbine were compared to cisplatin and paclitaxel using a human ovarian cancer xenografts model. Biopsy material from a native human ovarian carcinoma was expanded and transplanted into 96 nude mice. The animals were divided into six treatment groups: cisplatin 3 x 4 mg/kg, paclitaxel 5 x 26 mg/kg, vinorelbine 1 x 20 mg/kg, titanocene dichloride 3 x 30 mg/kg, titanocene dichloride 3 x 40 mg/kg and a control group treated with 0.9% saline. Each experiment was repeated with eight mice in each treatment group. Treatment groups were evaluated in terms of average daily increase in tumor volume and average daily body weight increase of nude mice based on slopes of least-square regressions performed on individual animals. The slope factors alpha and beta of the body weight (alpha) and tumor volume changes (beta) within each group during the course of an experiment were calculated. Both a statistically significant decrease (p<0.05) in the body weight of the experimental animals (cisplatin: alpha = -0.5163, vinorelbine: alpha = -0.6598, paclitaxel: alpha = -0.6746, titanocene dichloride 3 x 30 mg/kg: alpha = -0.6259, titanocene dichloride 3 x 40 mg/kg: alpha = -0.7758) and a significant reduction (p<0.05) of the increase in tumor volume (cisplatin: beta = 12.049, vinorelbine: beta = 0.504, paclitaxel: beta = -1.636, titanocene dichloride 3 x 30 mg/kg: beta = 6.212, titanocene dichloride 3 x 40 mg/kg: beta= -0.685) was shown in all treated groups compared to the control group (alpha = -0.1398; beta = 23.056). No significant weight changes were observed between the individually treated groups. A statistically significant reduction of the tumor growth occured under paclitaxel (beta = -1.636), vinorelbine (beta = 0.504) and titanocene dichloride medication 3 x 40 mg/kg (beta = -0.685), as compared to the group treated with cisplatin (beta = 12.049). We found titanocene dichloride to be as effective as paclitaxel and more effective than cisplatin. Vinorelbine seems to be a very effective antineoplastic agent exhibiting a significant higher cytostatic effect than cisplatin. Both titanocene dichloride and vinorelbine provide new therapeutic options in women with ovarian carcinoma not responding to standard chemotherapy.
Polyubiquitination of Transforming Growth Factor β (TGFβ)-associated Kinase 1 Mediates Nuclear Factor-κB Activation in Response to Different Inflammatory Stimuli (2011)

The transcription factor nuclear factor κB (NF-κB) plays a central role in regulating inflammation in response to several external signals. The TGFβ-associated kinase 1 (TAK1) is an upstream regulator of NF-κB signaling. In TGFβ-stimulated cells, TAK1 undergoes Lys-63-linked polyubiquitination at Lys-34 by TNF receptor-associated factor 6 and is thereby activated. The aim of this study was to investigate whether TAK1 polyubiquitination at Lys-34 is also essential for NF-κB activation via TNF receptor, IL-1 receptor and toll-like receptor 4. We observed that TAK1 polyubiquitination occurred at Lys-34 and required the E3 ubiquitin ligase TNF receptor-associated factor 6 after stimulation of cells with IL-1β. Polyubiquitination of TAK1 also occurred at Lys-34 in cells stimulated by TNF-α and LPS, which activates TLR4, as well as in HepG2 and prostate cancer cells stimulated with TGFβ, which in all cases resulted in NF-κB activation. Expression of a K34R-mutant TAK1 led to a reduced NF-κB activation, IL-6 promoter activity, and proinflammatory cytokine secretion by TNF-α-stimulated PC-3U cells. Similar results were obtained in the mouse macrophage cell line RAW264.7 after LPS treatment. In conclusion, polyubiquitination of TAK1 is correlated with activation of TAK1 and is essential for activation of NF-κB signaling downstream of several receptors.