gebhart/patrepeval huggingface dataset:
Tau stabilizes microtubules by binding at the interface between tubulin heterodimers (2015)

The structure, dynamic behavior, and spatial organization of microtubules are regulated by microtubule-associated proteins. An important microtubule-associated protein is the protein Tau, because its microtubule interaction is impaired in the course of Alzheimer's disease and several other neurodegenerative diseases. Here, we show that Tau binds to microtubules by using small groups of evolutionary conserved residues. The binding sites are formed by residues that are essential for the pathological aggregation of Tau, suggesting competition between physiological interaction and pathogenic misfolding. Tau residues in between the microtubule-binding sites remain flexible when Tau is bound to microtubules in agreement with a highly dynamic nature of the Tau-microtubule interaction. By binding at the interface between tubulin heterodimers, Tau uses a conserved mechanism of microtubule polymerization and, thus, regulation of axonal stability and cell morphology.
A Histidine-Rich Extensin from Zea mays Is an Arabinogalactan Protein (1992)

Earlier we isolated a threonine-rich extensin from maize (Zea mays). Here, we report that maize cell suspension cultures yield a new extensin rich in histidine (HHRGP) that also has characteristics of arabinogalactan proteins (AGPs). Thus, chymotryptic peptide maps of anhydrous hydrogen fluoride (HF)-deglycosylated HHRGP showed repetitive motifs related to both extensins and AGPs as follows. HHRGP contains Ala-Hyp(3) and Ala-Hyp(4) repeats that may be related to the classical dicot Ser-Hyp(4) extensin motif by the single T --> G (Ser --> Ala) base change. Furthermore, HHRGP also contains the repetitive motif Ala-Hyp-Hyp-Hyp-His-Phe-Pro-Ser-Hyp-Hyp related to the Ser-Hyp(4)-Ser-Hyp-Ser-Hyp(4) motif of P3-type dicot extensin. However, HHRGP also has AGP characteristics, notably an elevated alanine content, near sequence identity with the known Lolium AGP peptide Ser-Hyp-Hyp-Ala-Pro-Ala-Pro, the putative presence of glucuronoarabinogalactan, and precipitation by Yariv antigen, but beta-elimination of arabinogalactan indicates its O-linkage to serine rather than the characteristic O-hydroxyproline link of other AGPs. Although HHRGP might be a "chimera" of two different proteins, i.e. an extensin and an AGP, this is unlikely because one can account for the apparent chimera by the codon relationships of the five common hydroxyproline-rich glycoprotein amino acid residues, Ser, Pro, Thr, Ala (TCx, CCx, ACx, GCx) and histidine (CAT or CAC), which facilitate interconversion of major motifs by single point mutations. Thus, we propose that the extensin family of wall proteins consists of a highly diversified phylogenetic series ranging from basic minimally glycosylated repetitive pro-rich proteins to the highly glycosylated acidic AGPs. To relate this diversity of form and function at the molecular level, we identified putative functional domains hypothetically involved in properties such as reptation, recognition, adhesion, intermolecular cross-linkage, and self-assembly. Not previously noted, peptide palindromes feature prominently in HHRGP: Hyp-Hyp-Ala-Ala-Asn-Ala-Ala-Hyp-Hyp and Hyp-Hyp-Hyp-His-His-His-Hyp-Hyp-Hyp; in P3: Hyp(4)-Ser-Hyp-Ser-Hyp(4), and in other extensins. Such palindromes would enhance glycoprotein stereoregularity, thereby possibly promoting quasicrystalline interactions between wall components.
Host Cell Contact-Induced Transcription of the Type IV Fimbria Gene Cluster of Actinobacillus pleuropneumoniae (2004)

Type IV pili (Tfp) of gram-negative species share many characteristics, including a common architecture and conserved biogenesis pathway. Much less is known about the regulation of Tfp expression in response to changing environmental conditions. We investigated the diversity of Tfp regulatory systems by searching for the molecular basis of the reported variable expression of the Tfp gene cluster of the pathogen Actinobacillus pleuropneumoniae. Despite the presence of an intact Tfp gene cluster consisting of four genes, apfABCD, no Tfp were formed under standard growth conditions. Sequence analysis of the predicted major subunit protein ApfA showed an atypical alanine residue at position -1 from the prepilin peptidase cleavage site in 42 strains. This alanine deviates from the consensus glycine at this position in Tfp from other species. Yet, cloning of the apfABCD genes under a constitutive promoter in A. pleuropneumoniae resulted in pilin and Tfp assembly. Tfp promoter-luxAB reporter gene fusions demonstrated that the Tfp promoter was intact but tightly regulated. Promoter activity varied with bacterial growth phase and was detected only when bacteria were grown in chemically defined medium. Infection experiments with cultured epithelial cells demonstrated that Tfp promoter activity was upregulated upon adherence of the pathogen to primary cultures of lung epithelial cells. Nonadherent bacteria in the culture supernatant exhibited virtually no promoter activity. A similar upregulation of Tfp promoter activity was observed in vivo during experimental infection of pigs. The host cell contact-induced and in vivo-upregulated Tfp promoter activity in A. pleuropneumoniae adds a new dimension to the diversity of Tfp regulation.
Characterization and Regulation of the Receptor Tyrosine Kinase Tie-1 in Platelets (2000)

The receptor tyrosine kinase Tie-1 is expressed predominantly on endothelial cells where it has an essential role in blood vessel formation. Targeted disruption of the Tie-1 gene results in a lethal phenotype with severe disruption to the normal integrity of the vasculature. In an examination of Tie-1 in vivo, we observed a significant pool of the receptor present in the circulation associated with the platelet fraction. Western blotting reveals the platelet form of Tie-1 to be a protein of approximately 110 kDa, this contrasts with the 135/125-kDa doublet found in endothelial cells. Platelet activation results in increased surface expression of Tie-1. The closely related receptor tyrosine kinase Tie-2/Tek is not present in platelets. Endothelial Tie-1 undergoes metalloprotease-mediated ectodomain cleavage in response to phorbol ester and other agonists. Tie-1 cleavage leads to release of the extracellular domain and generation of a cell-associated intracellular domain with signalling capacity. The potential for cleavage was investigated in platelets. In contrast to endothelial Tie-1, phorbol ester does not stimulate truncation of the platelet receptor, suggesting these cells lack one or more components of the regulated metalloprotease system controlling Tie-1. These data demonstrate the Tie-1 receptor tyrosine kinase is present on platelets and its surface expression is regulated. Furthermore, platelet Tie-1 differs significantly from the endothelial receptor. Platelet Tie-1 has the potential to modulate endothelial function by competing for any Tie ligands and may have signalling roles important in controlling aspects of platelet behaviour.
ADP ribosylation of human neutrophil peptide-1 regulates its biological properties (2002)

In human airways, epithelial cells lining the lumen and intraluminal cells (e.g., polymorphonuclear cells) participate in the innate immune response. These cells secrete or express on their surfaces arginine-specific ADP ribosyltransferases. Defensins, antimicrobial proteins secreted by immune cells, are arginine-rich, leading us to hypothesize that ADP ribosylation could modify their biological activities. We found that an arginine-specific ADP ribosyltransferase-1 present on airway epithelial cells modifies Arg-14 of alpha defensin-1. ADP-ribosylated defensin-1 had decreased antimicrobial and cytotoxic activities but still stimulated T cell chemotaxis and IL-8 release from A549 cells. Further, ADP-ribosylated defensin-1 inhibited cytotoxic and antimicrobial activities of unmodified defensin-1. We identified ADP-ribosylated defensin-1 in bronchoalveolar lavage fluid from smokers but not from nonsmokers, confirming its existence in vivo. Thus, airway mono-ADP-ribosyltransferases could have an important regulatory role in the innate immune response through modification of alpha defensin-1 and perhaps other basic molecules, with alteration of their biological properties.
Application of Predictive QSAR Models to Database Mining:  Identification and Experimental Validation of Novel Anticonvulsant Compounds (2004)

We have developed a drug discovery strategy that employs variable selection quantitative structure-activity relationship (QSAR) models for chemical database mining. The approach starts with the development of rigorously validated QSAR models obtained with the variable selection k nearest neighbor (kNN) method (or, in principle, with any other robust model-building technique). Model validation is based on several statistical criteria, including the randomization of the target property (Y-randomization), independent assessment of the training set model's predictive power using external test sets, and the establishment of the model's applicability domain. All successful models are employed in database mining concurrently; in each case, only variables selected as a result of model building (termed descriptor pharmacophore) are used in chemical similarity searches comparing active compounds of the training set (queries) with those in chemical databases. Specific biological activity (characteristic of the training set compounds) of external database entries found to be within a predefined similarity threshold of the training set molecules is predicted on the basis of the validated QSAR models using the applicability domain criteria. Compounds judged to have high predicted activities by all or the majority of all models are considered as consensus hits. We report on the application of this computational strategy for the first time for the discovery of anticonvulsant agents in the Maybridge and National Cancer Institute (NCI) databases containing ca. 250,000 compounds combined. Forty-eight anticonvulsant agents of the functionalized amino acid (FAA) series were used to build kNN variable selection QSAR models. The 10 best models were applied to mining chemical databases, and 22 compounds were selected as consensus hits. Nine compounds were synthesized and tested at the NIH Epilepsy Branch, Rockville, MD using the same biological test that was employed to assess the anticonvulsant activity of the training set compounds; of these nine, four were exact database hits and five were derived from the hits by minor chemical modifications. Seven of these nine compounds were confirmed to be active, indicating an exceptionally high hit rate. The approach described in this report can be used as a general rational drug discovery tool.
Sympathetic overactivity in renal failure controlled by ACE inhibition: clinical significance (2000)

member of the polyoma virus family causes interstitial nephritis, transplant recipients and in pregnant women, which ureteritis, and enteritis in immunosuppressed cynomolgus monare almost always due to reactivation of latent BKV. keys. Am J Pathol 1999; 154: 1273–1284 Furthermore, as shown in Table 1, BKV infection in 4. Nickeleit V, Hirsch HH, Zeiler M, Gudat F, Prince O, Thiel G, renal transplant recipients occurs most frequently when Mihatsch MJ. BK-virus nephropathy in renal transplants: Tubular necrosis, MHC-class II expression and rejection in a kidney from a BKV-seropositive donor is transplanted puzzling game. Nephrol Dial Transplant 2000; 15: 323–331 into a BKV seronegative recipient. Such a donor/ 5. Randhawa PS, Finkelstein S, Scantlebury V et al. Human recipient antibody combination may be a risk factor polyoma virus-associated interstitial nephritis in the allograft for BKV nephropathy. kidney. Transplantation 1999; 67: 103–109 6. Binet I, Nickeleit V, Hirsch HH et al. Polyomavirus disease under new immunosuppressive drugs. Transplantation 1999; 67: 918–922 References 7. Drachenberg CB, Beskow CO, Cangro CB et al. Human polyoma virus in renal allograft biopsies: Morphological findings 1. Shah KV. Polyomaviruses. In: Fields BN, Kipe DM, Howley and correlation with urine cytology. Hum Pathol 1999; 30: PM et al., eds, Fields Virology, 3rd edn. Lippincot-Raven 970–977 Publishers, Philadelphia: 1996: 2027–2043 8. Andrews CA, Daniel RW, Shah KV. Serologic studies of 2. Horvath CJ, Simon MA, Bergsagel DJ et al. Simian virus papovavirus infections in pregnant women and renal transplant 40-induced disease in rhesus monkeys with simian acquired recipients. In: Sever JL, Madden DL, eds, Progress in Clinical immunodeficiency syndrome. Am J Pathol 1992; 140: 1431–1440 and Biological Research, Vol. 105, Alan R. Liss, Inc., New York: 3. van Gorder MA, della Pelle P, Henson JW, Sachs DH, Cosimi AB, Colvin RB. Cynomolgus polyoma virus infection. A new 1983: 133–141
ICE-BA: Incremental, Consistent and Efficient Bundle Adjustment for Visual-Inertial SLAM (2018)

Modern visual-inertial SLAM (VI-SLAM) achieves higher accuracy and robustness than pure visual SLAM, thanks to the complementariness of visual features and inertial measurements. However, jointly using visual and inertial measurements to optimize SLAM objective functions is a problem of high computational complexity. In many VI-SLAM applications, the conventional optimization solvers can only use a very limited number of recent measurements for real time pose estimation, at the cost of suboptimal localization accuracy. In this work, we renovate the numerical solver for VI-SLAM. Compared to conventional solvers, our proposal provides an exact solution with significantly higher computational efficiency. Our solver allows us to use remarkably larger number of measurements to achieve higher accuracy and robustness. Furthermore, our method resolves the global consistency problem that is unaddressed by many state-of-the-art SLAM systems: to guarantee the minimization of re-projection function and inertial constraint function during loop closure. Experiments demonstrate our novel formulation renders lower localization error and more than 10x speedup compared to alternatives. We release the source code of our implementation to benefit the community <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Energy Analysis of Public-Key Cryptography for Wireless Sensor Networks (2005)

In this paper, we quantify the energy cost of authentication and key exchange based on public-key cryptography on an 8-bit microcontroller platform. We present a comparison of two public-key algorithms, RSA and elliptic curve cryptography (ECC), and consider mutual authentication and key exchange between two untrusted parties such as two nodes in a wireless sensor network. Our measurements on an Atmel ATmega128L low-power microcontroller indicate that public-key cryptography is very viable on 8-bit energy-constrained platforms even if implemented in software. We found ECC to have a significant advantage over RSA as it reduces computation time and also the amount of data transmitted and stored.
The influence of carbon fibres on the resorption time and mechanical properties of the lactide–glycolide co-polymer (2007)

In this study the influence of short carbon fibres (CF) on mechanical properties and degradation time of the lactide-glycolide co-polymer (PGLA) and on the mechanism of bone ingrowth into the implants was determined. Mechanical properties and push-out tests were measured. The pH of solutions and the implants' weights were tested after incubation in Ringer fluid. Analysis was based upon FT-IR and SEM with EDS studies. Pathological examinations were also performed. The in vitro examination revealed that carbon fibres accelerated polymer degradation process and increased the mechanical strength of polymer. In the case of PGLA + CF under in vivo conditions, initially, the superficial polymer degradation with new tissue in-growth was observed. Next, the degradation process included also the inner part of the implant, while the bone began to grow on exposed carbon fibres. In the case of pure PGLA the growth of soft tissue can be observed at the bone-implant interface and in the implant area. Our research indicates that PGLA + CF composite can be used in bone surgery as a short-term multifunctional load-bearing implant, which initially provides a mechanical support. During the time of controlled resorption of PGLA, carbon fibres act as a scaffold for the bone growth.
Spider‐Web‐Inspired PM0.3 Filters Based on Self‐Sustained Electrostatic Nanostructured Networks (2020)

In addition, in Figure The correct image for the fourth image in 2f, for DTAB concentration of 4.0, together with its inset is shown below.
Phosphorylcholine-coated stents in porcine coronary arteries: in vivo assessment of biocompatibility. (2001)

The divYsio stents, with or without PC coating, performed equally well in terms of acute patency, 28-day QCA and morphometry. The PC coating allows a stent to endothelialize normally and is not associated with specific histological changes. The PC coating on the divYsio stent appears biocompatible.
An Experimental Study of Membrane Materials and Inner Contacting Layers for Ion-Selective K+ Electrodes with a Stable Response and Good Dynamic Range (2004)

The goal was to identify formulations for use in valinomycin K(+) ion-selective electrodes that could routinely achieve a detection limit of <10(-6) M, even after repeated use and exposure at higher K+ activity (0.1 M) and without the requirement for special pretreatment or conditioning in low K+ activity (10(-3) M). Electrodes that would be characterized by high potential stability were sought in this work. Valinomycin-containing membranes with diffusion coefficient of approximately 10(-11) cm(2) s(-1), formulated from methacrylic/acrylic polymers with or without plasticizer, were compared with plasticized PVC membranes (diffusion coefficient 10(-8) cm(2) s(-1)). The methacrylic/acrylic membranes without plasticizer were shown to give an order of magnitude lower detection limit, when compared with PVC-dioctyl sebacate and o-nitrophenyl octyl ether plasticized methacrylic/acrylic polymers under the same conditions, highlighting the influence of plasticizer on the detection limit. As predicted from current theoretical derivation, the inner contacting layer in the ion-selective electrode construction was shown to be highly influential in maintaining the detection limit below 10(-6) M with use and with poly(pyrrole) providing the inner contact ion-to-electron transduction function, a further order of magnitude improvement in the lower detection limit could be maintained for both chloride and hexacyanoferrate doped poly(pyrrole), when 2% ionophore was employed in the ion-selective membrane. This formulation showed extraordinary stability and reproducibility in terms of measurement range and drift over extended measurement testing, with close to Nernstian slopes. At higher ionophore concentrations (4%), the apparent selectivity of the electrode was improved at the expense of detection limit and the nature of the poly(pyrrole) dopant ion became important in determining the dominant exchange processes at the poly(pyrrole)/ion-selective membrane interface.
Cytological and Molecular Analysis of the Hordeum vulgare-Puccinia triticina Nonhost Interaction (2003)

Cultivated barley, Hordeum vulgare L., is considered to be a nonhost or intermediate host species for the wheat leaf rust fungus Puccinia triticina. Here, we have investigated, at the microscopic and molecular levels, the reaction of barley cultivars to wheat leaf rust infection. In the nonhost resistant cultivar Cebada Capa, abortion of fungal growth occurred at both pre- and posthaustorial stages, suggesting that defense genes are expressed throughout the development of the inappropriate fungus during the nonhost resistance reaction. In the two barley lines L94 and Bowman, a low level of prehaustorial resistance to P. triticina was observed and susceptibility was comparable to that of wheat control plants. Suppression subtractive hybridization was used to identify genes that are differentially expressed during the nonhost resistance reaction in Cebada Capa as well as during the successful establishment of the inappropriate wheat leaf rust fungus in L94. Northern analysis indicated that two candidate genes, including a barley ortholog of the rice resistance gene Xa21, are putatively involved in nonhost and non-race-specific resistance reactions. In addition, a new gene that is specifically induced during the successful development of the inappropriate fungus P. triticina in barley has been identified.
13 The Double-stranded RNA-activated Protein Kinase PKR (2000)

Cells respond to environmental stress by immediate changes in their capacity and specificity to select mRNAs for translation. Most translational control occurs at the level of initiation. The rate of translation initiation depends on mRNA abundance, the number of ribosomes, the availability of initiator tRNA i Met , and the amount and activity of eukaryotic translation initiation factors (eIFs). Reversible covalent modification of these eIFs is a fundamental mechanism that determines the rate of initiation. One modification used for translational control in response to environmental stress is the reversible phosphorylation of eIF2. Phosphorylation of heterotrimeric eIF2 on the α subunit (eIF2α) rapidly reduces the level of functional eIF2 and limits initiation events on all cellular mRNAs within the cell. In higher eukaryotes, it is not known whether some mRNAs are selectively translated when eIF2 is inactivated by phosphorylation, as demonstrated for the Saccharomyces cerevisiae mRNA encoding GCN4 (see Chapter 5). Reversible phosphorylation of eIF2α provides the cell with an efficient, rapid, and reversible means to respond to a variety of different stimuli. Initiation of polypeptide chain synthesis requires the recycling of eIF2 between GTP- and GDP-bound states in a reaction catalyzed by the guanine nucleotide exchange factor, eIF2B (for review, see Pain 1996; Chapters 2 and 5). Phosphorylation of eIF2α at residue Ser-51 stabilizes the eIF2/GDP/eIF2B complex and prevents the GDP–GTP exchange reaction. Because the cellular levels of eIF2B are lower than the levels of eIF2 (Oldfield et al. 1994), the exchange process is inhibited when only a fraction (i.e., 20–30%)...
Enantioselective Formal [4 + 2] Annulation of ortho-Quinone Methides with ortho-Hydroxyphenyl α,β-Unsaturated Compounds (2018)

The highly efficient enantioselective [4 + 2] cycloaddition of o-QMs with ortho-hydroxyphenyl-substituted α,β-unsaturated compounds was realized by using a chiral N, N'-dioxide-Sc(III) complex as catalyst. A variety of chiral chromane derivatives with three continuous stereocenters were obtained in excellent results (up to 99% yield, >19:1 dr, and 99% ee) under as low as 0.005-1 mol % catalyst loading. Besides, a catalytic cycle with a possible transition state model was proposed to elucidate the origin of the chirality.