gebhart/patrepeval huggingface dataset:
Flanking sequence preference modulates de novo DNA methylation in the mouse genome (2020)

Abstract Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences are not mediated by the differential recruitment of the two de novo DNMTs to the genome but are resulting from structural differences in their catalytic domains. Molecular dynamics simulations suggest that, in case of DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. This context-dependent de novo DNA methylation provides additional insights into the complex regulation of methylation patterns in different cell types.
A Particle Filter SLAM Approach to Online Iceberg Drift Estimation From an AUV (2017)

Using autonomous underwater vehicles (AUVs) for mapping the underwater topography of sea-ice and icebergs, or detecting keels of ice ridges, is foreseen as an enabling technology in future Arctic offshore operations. This paper presents a method for online iceberg drift estimation using a Simultaneous Localization and Mapping (SLAM) approach using an AUV with a multi-beam echosounder (MBE) during such survey/monitoring operations. Iceberg drift is affected by wind, current, and Coriolis forces. This can be hard to predict, making automated mapping of icebergs difficult. The method proposed in this paper estimates the iceberg’s pose using a particle filter, where each particle uses extended information filters to estimate the topography of the iceberg. A grid map is used to store the iceberg topography, and distributed particle mapping is used to avoid expensive copy operations during particle resampling. The proposed method is verified through a simulation study, using a 6 DOF AUV model, an MBE sensor model, and an iceberg topography taken from the PERD iceberg sightings database. The method is able to provide a georeferenced iceberg position, thus, estimating the iceberg’s drift trajectory. A topography estimate of the iceberg, corrected for iceberg drift, is also generated. Furthermore, the algorithm estimates the iceberg drift velocity, as well as the relative iceberg-AUV pose, for use in future iceberg mapping guidance algorithms. The simulation study illustrates the performance of the method, and a short execution time analysis is presented to illustrate the method’s real-time potential.
Antimicrobial Activity of Rifabutin (1996)

Rifabutin is a spiro-piperidyl-rifamycin derived from rifamycin-S. It is structurally related to rifampin and shares many of its properties. Rifabutin has a broad spectrum of antimicrobial activity. It is considerably more active than rifampin in vitro against the Mycobacterium avium complex (MAC), Mycobacterium tuberculosis, and Mycobacterium leprae. It also is active against most atypical mycobacteria, including Mycobacterium kansasii, but Mycobacterium chelonae is relatively resistant. Rifabutin also is active against staphylococci, group A streptococci, Neisseria gonorrhoeae, Neisseria meningitidis, Haemophilus influenzae, Haemophilus ducreyi, Campylobacter jejuni, Helicobacter pylori, Chlamydia trachomatis, and Toxoplasma gondii. It has poor activity against Enterobacteriaceae and Pseudomonas species. This review focuses on the antimicrobial profile of rifabutin in relation to its pharmacological properties. Special emphasis is placed on its in vitro activity against MAC and other mycobacteria, its efficacy in cell culture and animal models, and its potential as a component of multidrug therapy for mycobacterial and other infectious diseases.
Photochemical Cells Sensitized by Lignophenol Derivatives (2007)

Hinoki cypress (Chamaecyparis obtusa)-lignophenol(p-cresol type, HCLC) have been directly synthesized from lignocellulosics through the phase-separation system, which were surface reactions between 72 % H 2 S0 4 and p-cresol under 1 atm at 30 C. Because of rich phenolic hydroxyl groups in grafted phenols, various derivatives were designed from LPs. In the case of phenolic hydroxyl groups on ortho-positions for C 1 -carbons in phenylpropane units in the native lignins, the function groups acted as recycling switches for cleavages of main chains of LPs under alkaline conditions with heat. Resulting derivatives (2nd der.) have showed new features in addition to properties of HCLC. Hydroxymathylation of HCLC (HCLC-HM) were easily carried out by treatment of methanal under alkaline conditions (60 C). Resulting HCLC-HM were polymelyzed into network type derivatives (HCLC-HM-P) by heat treatments. HCLC-HM, HCLC-HM-P and their 2nd der. showed visible light conversion into electricity on the nano-Ti0 2 electrodes. Especially 2nd der. showed good result (Voc = 0.47 V, lsc = 3.17 mAcm-2 , FF = 0.74 and l')= 0.89%) probably because both absorption of light and adsorption on the electrodes were improved by productions of quinoid type structures on HCLC by alkaline treatments.
Cell‐Mediated Cytotoxicity in Lyme Arthritis (2022)

We propose that CD8+ T cell-mediated cytotoxicity, CD4+ T cell help, autoantibodies to vascular antigens, and complement deposition may each have a role in microvasculature damage in post-antibiotic LA.
In vivo quantification of Bruch's membrane in humans with visible light OCT (Conference Presentation) (2020)

Bruch’s membrane (BM) and retinal pigment epithelium (RPE) changes, thought to be the earliest signs of impending atrophy in dry age-related macular degeneration (AMD), are subtle and challenging to detect non-invasively. Here, we demonstrate imaging and quantification of BM and RPE thickness in the in vivo human eye using achromatized visible light optical coherence tomography (OCT) in normal human subjects. Our consistent visualization of BM and agreement of thickness values with ranges from prior histological studies is attributed to the increased axial resolution, and potentially also to the enhanced contrast of BM in the visible light range.
ChemInform Abstract: Enantioselective Aza‐Diels—Alder Reaction of Aldimines with “Danishefsky‐Type Diene” Catalyzed by Chiral Scandium(III)‐N,N′‐Dioxide Complexes. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Dehydrothalebanin:  A Source of Resistance from Glycosmis pentaphylla against the Citrus Root Weevil Diaprepes abbreviatus (2000)

Roots of a citrus relative, Glycosmis pentaphylla (orangeberry), were shown to inhibit the growth and survival of larvae of the citrus root weevil Diaprepes abbreviatus. Roots of G. pentaphyllaincorporated into the diet of D. abbreviatus increasingly inhibited the growth of neonate larvae with increased concentration of roots, while roots from citrus rootstocks produced little inhibition. The diet-incorporation assay was used to guide fractionation of an active acetone extract of G.pentaphylla roots. Three major fractions from silica open-column liquid chromatography were active, and these were purified using semipreparative normal-phase HPLC. A single active HPLC subfraction was isolated from each of the three liquid chromatography fractions, and two active compounds were isolated and identified by GC-MSD. GC-MSD and NMR identified one compound as the amide dehydrothalebanin B, and the other was identified by GC-MSD as dieldrin, a chlorinated hydrocarbon insecticide whose origin in our samples is uncertain.
Mechanisms of Antioxidant Action: The Antioxidant Activity of “Spin-Traps” in Rubber (1984)

Abstract A number of nitrones containing a partially hindered phenolic group are shown to be effective antidegradants for sulfur vulcanized rubbers. They exhibit a high level of antiozonant and antifatigue activity, but unlike commercial antiozonants they do not cause discoloration of light colored formulations. The new antidegradants are less effective than conventional additives as thermal antioxidants, but their performance as antifatigue agents and antioxidants is augmented by their use in combination with nonstaining antioxidants. The mechanism of action of the phenolic nitrones is believed to involve their oxidation to stable phenoxyl/nitroxyl radicals.
Histochemical Localization of Citral Accumulation in Lemongrass Leaves (Cymbopogon citratus(DC.) Stapf., Poaceae) (1998)

Lemongrasses (Cymbopogon spp., Poaceae) are a group of commercially important C % tropical grasses. Their leaves contain up to 1n5 % (d.wt) essential oils with a typical lemon-like aroma, consisting mainly of citral (a mixture of the isomeric acyclic monoterpene aldehydes geranial and neral). To specifically locate the sites of citral accumulation in lemongrass we employed Schiff's reagent, which reacts with aldehydes and gives a purple-red coloration with citral. Using this technique, single oil-accumulating cells were detected in the adaxial side of leaf mesophyll, commonly adjacent to non-photosynthetic tissue, and between vascular bundles. Cell walls of these oil cells are lignified. Our results suggest that citral accumulation takes place in individual oil cells within the leaf tissues.
A HYPOTHESIS OF RADIORESISTANCE AND CELL-SURVIVAL CURVE SHAPE BASED ON CELL-CYCLE PROGRESSION AND DAMAGE TOLERANCE (2018)

Exponential survival curves of early-passage human fibroblasts challenge classic biophysical models of cell inactivation. Thus, X-ray doses of 2-4 Gy inactivate normal, human skin fibroblasts in spite of negligible residual double-strand breaks. By contrast, radioresistant p53-mutant U251 glioblastoma cells proliferate in spite of residual damage. Similarly, p53 wildtype TK6 lymphoblastoid cells show exponential survival curves while the related p53-mutant WTK1 cell line continued to proliferate and showed a shouldered survival curve. Here, we propose a model in which the radioresistant shoulder region is due to tolerance to certain types or amounts of residual damage that would otherwise inactivate normal cells. Thus, the steeper initial slope and absence of a shoulder in the survival curve of normal cells may not imply a higher number of residual lesions but rather non-tolerance to these lesions.
Component-Based Safety Computer of Railway Signal Interlocking System (2008)

Computer is the vital element for safety-critical control system. This paper presents a component-based fail-safe computer in railway signal interlocking system (safety interlock computer - SIC). We discuss the methodology and the safety tactics of SIC in detail, moreover, the architecture and safety computation principle are deeply analyzed. The hardware safety integrity level of SIC has been verified according to standard IEC 61508, and the result shows that SIL4 is achieved, and SIC fulfils the rigorous safety requirements of signal interlocking.
DroneNavigator (2015)

Even after decades of research about navigation support for visually impaired people, moving independently still remains a major challenge. Previous work in HCI explored a large number of navigation aids, including auditory and tactile guidance systems. In this poster we propose a novel approach to guide visually impaired people. We use small lightweight drones that can be perceived through the distinct sound and the airflow they naturally produce. We describe the interaction concept we envision, first insights from proof-of-concept tests with a visually impaired participant, and provide an overview of potential application scenarios.
Does Pet Arrival Trigger Prosocial Behaviors in Individuals with Autism? (2012)

Alteration of social interactions especially prosocial behaviors--an important aspect of development--is one of the characteristics of autistic disorders. Numerous strategies or therapies are used to improve communication skills or at least to reduce social impairments. Animal-assisted therapies are used widely but their relevant benefits have never been scientifically evaluated. In the present study, we evaluated the association between the presence or the arrival of pets in families with an individual with autism and the changes in his or her prosocial behaviors. Of 260 individuals with autism--on the basis of presence or absence of pets--two groups of 12 individuals and two groups of 8 individuals were assigned to: study 1 (pet arrival after age of 5 versus no pet) and study 2 (pet versus no pet), respectively. Evaluation of social impairment was assessed at two time periods using the 36-items ADI-R algorithm and a parental questionnaire about their child-pet relationships. The results showed that 2 of the 36 items changed positively between the age of 4 to 5 (t(0)) and time of assessment (t(1)) in the pet arrival group (study 1): "offering to share" and "offering comfort". Interestingly, these two items reflect prosocial behaviors. There seemed to be no significant changes in any item for the three other groups. The interactions between individuals with autism and their pets were more--qualitatively and quantitatively--reported in the situation of pet arrival than pet presence since birth. These findings open further lines of research on the impact of pet's presence or arrival in families with an individual with autism. Given the potential ability of individuals with autism to develop prosocial behaviors, related studies are needed to better understand the mechanisms involved in the development of such child-pet relationship.
Clinical application of the lens haptic plane concept with transformed axial lengths (2005)

The LHP concept in combination with thick-lens ray tracing achieved MAE comparable to that with currently used formulas. The lack of trend with axial length is important for patients with short and long eyes.
Selective Photoreceptor Gene Knock‐out Reveals a Regulatory Role for the Growth Behavior of Pseudomonas syringae (2016)

The plant pathogen Pseudomonas syringae (Ps) is a well-established model organism for bacterial infection of plants. The genome sequences of two pathovars, pv. syringae and pv. tomato, revealed one gene encoding a blue and two genes encoding red/far red light-sensing photoreceptors. Continuing former molecular characterization of the photoreceptor proteins, we here report selective photoreceptor gene disruption for pv. tomato aiming at identification of potentially regulatory functions of these photoreceptors. Transformation of Ps cells with linear DNA constructs yielded interposon mutations of the corresponding genes. Cell growth studies of the generated photoreceptor knock-out mutants revealed their role in light-dependent regulation of cell growth and motility. Disruption of the blue-light (BL) receptor gene caused a growth deregulation, in line with an observed increased virulence of this mutant (Moriconi et al., Plant J., 2013, 76, 322). Bacterial phytochrome-1 (BphP1) deletion mutant caused unaltered cell growth, but a stronger swarming capacity. Inactivation of its ortholog, BphP2, however, caused reduced growth and remarkably altered dendritic swarming behavior. Combined knock-out of both bacteriophytochromes reproduced the swarming pattern observed for the BphP2 mutant alone. A triple knock-out mutant showed a growth rate between that of the BL (deregulation) and the phytochrome-2 mutant (growth reduction).
Development of a novel aortic dissection mouse model and evaluation of drug efficacy using in-vivo assays and database analyses (2018)

Our results suggest that endothelial dysfunction is associated with the onset of aortic dissection and pitavastatin can help prevent this condition.
Thy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis (2022)

The presence of distinct stem cells that maintain the interfollicular epidermis is highly debated. Here, we report a population of keratinocytes, marked by Thy1, in the basal layer of the interfollicular epidermis. We find that epidermal cells expressing differential levels of Thy1 display distinct transcriptional signatures. Thy1<sup>+</sup> keratinocytes do not express T cell markers, express a unique transcriptional profile, cycle significantly slower than basal epidermal progenitors and display significant expansion potential in vitro. Multicolor lineage tracing analyses and mathematical modeling reveal that Thy1<sup>+</sup> basal keratinocytes do not compete neutrally alike interfollicular progenitors and contribute long-term to both epidermal replenishment and wound repair. Importantly, ablation of Thy1<sup>+</sup> cells strongly impairs these processes, thus indicating the non-redundant function of Thy1<sup>+</sup> stem cells in the epidermis. Collectively, these results reveal a distinct stem cell population that plays a critical role in epidermal homeostasis and repair.
Variable-length instruction compression for area minimization (2004)

Memories comprise a significant part of chips in embedded applications, thus also contributing considerably to the costs. We present a variable-length compression scheme for reducing program memory footprint in a 32-bit DSP processor. The compression method is based on a static program code analysis. Short operand fields do not provide sufficient repetition individually, so the compression is realized by handling all operands of an instruction as one field. The more a certain operand combination is used, the shorter it is coded. The original combination is placed on a look-up table and the coded bit pattern forms an index to that table. The compression results that are achieved in two test applications are 46% (audio decoder) and 51% (video decoder).
Wide Bite Angle Disphosphine Ligands in Thermally Activated Delayed Fluorescent Copper(I) Complexes: Impact on the Performance of Electroluminescence Applications (2021)

We report a series of seven cationic heteroleptic copper(I) complexes of the form [Cu (P^P) (dmphen)]BF4, where dmphen is 2,9-dimethyl-1,10-phenanthroline and P^P is a diphosphine chelate, in which the effect of the bite angle of the diphosphine ligand on the photophysical properties of the complexes was studied. Several of the complexes exhibit moderately high photoluminescence quantum yields in the solid-state, with ΦPL of up to 35%, and in solution, with ΦPL of up to 98%. We were able to correlate the powder photoluminescence quantum yields with the %Vbur of the P^P ligand. The most emissive complexes were used to fabricate both organic light-emitting diodes (OLEDs) and light-emitting electrochemical calls (LECs), both of which showed moderate performance. Compared to the benchmark Cu(I)-based LECs, [Cu(dnbp)(DPEPhos)]+ (EQEmax = 16%), complex 3 (EQEmax = 1.85%) showed much longer device lifetime (t1/2 = 1.25 h and >16.5 h for [Cu(dnbp)(DPEPhos)]+ and complex 3, respectively). The electrochemiluminescent properties of several complexes were also studied which to the best of our knowledge constitutes the first ECL study for heteroleptic copper (I) complexes. Notably, complexes exhibiting more reversible electrochemistry were associated with higher annihilation ECL as well as better performance in an LEC device.
Database-Guided Discovery of Potent Peptides to Combat HIV-1 or Superbugs (2013)

Antimicrobial peptides (AMPs), small host defense proteins, are indispensable for the protection of multicellular organisms such as plants and animals from infection. The number of AMPs discovered per year increased steadily since the 1980s. Over 2,000 natural AMPs from bacteria, protozoa, fungi, plants, and animals have been registered into the antimicrobial peptide database (APD). The majority of these AMPs (>86%) possess 11-50 amino acids with a net charge from 0 to +7 and hydrophobic percentages between 31-70%. This article summarizes peptide discovery on the basis of the APD. The major methods are the linguistic model, database screening, de novo design, and template-based design. Using these methods, we identified various potent peptides against human immunodeficiency virus type 1 (HIV-1) or methicillin-resistant Staphylococcus aureus (MRSA). While the stepwise designed anti-HIV peptide is disulfide-linked and rich in arginines, the ab initio designed anti-MRSA peptide is linear and rich in leucines. Thus, there are different requirements for antiviral and antibacterial peptides, which could kill pathogens via different molecular targets. The biased amino acid composition in the database-designed peptides, or natural peptides such as θ-defensins, requires the use of the improved two-dimensional NMR method for structural determination to avoid the publication of misleading structure and dynamics. In the case of human cathelicidin LL-37, structural determination requires 3D NMR techniques. The high-quality structure of LL-37 provides a solid basis for understanding its interactions with membranes of bacteria and other pathogens. In conclusion, the APD database is a comprehensive platform for storing, classifying, searching, predicting, and designing potent peptides against pathogenic bacteria, viruses, fungi, parasites, and cancer cells.
Chemical selectivity in the remote abstractive chemisorption of ICl on Al(111) (2000)

The interaction of ICl and Al(111) involves remote dissociation in its chemisorption process. In remote dissociation, an electron harpoons from an Al(111) surface to an ICl gas molecule to initiate the chemisorption process. We have determined that ICl can chemisorb onto Al(111) by non-activated direct chemisorption, and the sticking probability of this direct channel is 0.65 +/- 0.03. Furthermore, low energy ICl molecules that do not undergo remote dissociation can chemisorb onto Al(111) by precursor-mediated chemisorption. Not only is the interaction of ICl and Al(111) reactive, it is chemically selective. Studies with Auger spectroscopy reveal that the ratio of chlorine atoms to iodine atoms on the Al(111) is 0.32 +/- 0.10 at low (0.042 +/- 0.002) surface coverage. Time-of-flight mass spectrometry studies also show that chlorine atoms are the only species scattered from the surface after ICl interacts with Al(111). These results indicate that iodine-selective abstraction, in which the iodine atom of ICl chemisorbs to the aluminium surface while the chlorine atom is ejected into the gas phase, is the dominant mechanism in this reaction. Iodine-end first collisions are more reactive than chlorine-end first collisions because the lowest unoccupied molecular orbital (LUMO) of ICl is primarily composed of iodine atomic orbitals, and it is the LUMO that interacts with the harpooning electron from the aluminium.
Micro Secure Socket Layer for Micro Server (2010)

In this paper, we propose Micro Secure Socket Layer (MSSL) for 8-bit flash micro controller that is about 1.3 Kbytes in code size. We have analyzed and compared various cryptographic protocols in TCP/IP stack for 5$ Micro Server to propose a simple secure layer based on simple handshake processing and encryption. Additionally, we analyzed MSSL performance, compared with the current security protocols and proved that MSSL can secure the connection between Micro Server and Internet. Security implementation for Micro Server, which has very limited size of memory with a small processer, is very difficult and challenging task. Conventional researches have focused mainly on creating small sensor system and Micro Server that has multi-function with low cost and small memory size, but without much security considerations. Crackers can easily access to the sensor nodes or Micro Server. Therefore, minimum security is needed in the ubiquitous sensor networks. The proposed MSSL is very small in code size so it can be implemented and is suitable for small sensors and Micro Server systems.