gebhart/patrepeval huggingface dataset:
Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration (2006)

The analysis of alignments of functionally equivalent proteins can reveal regularities such as correlated positions or residue patterns which are important to ensure a specific fold and various cellular functions. Many approaches are found in the literature which try to identify correlated positions to predict the residues that are close to each other in the three-dimensional folded structure. However, the quality of the predictions remains disappointing. One of the problems is that the statistical correlation measures that were used cannot do justice to the underlying complex biological and physicochemical realities. In this paper we evaluate the biological requirements for a correlation measure and explain why a completely automatic approach is unlikely to succeed. We then propose a novel and flexible criteria for correlation of residue positions in protein sequences, which can be optimized for different requirements. To apply this definition we developed the tool VisAlign that combines an automatic calculation of correlations with an interactive visualization. This allows the user to visually explore alternative alignments and thereby conveniently test various hypothesis and to detect regularities in the aligned sequences
The Cardiovascular Burden of the Dialysis Patient: The Impact of Dialysis Technology (2005)

There is widespread recognition that the poor survival rates of dialysis patients, attributed predominantly to cardiovascular disease, need to be addressed and improved. In this paper, we relate diverse aspects of modern dialysis technology with factors that are considered to contribute towards increased mortality and morbidity in the dialysis population. Firstly, we assess the overall cardiovascular burden of the dialysis patient: it is the sum of uraemia-related risk factors (URRF), traditional risk factors and dialysis-therapy-related factors. Secondly, we describe how key components of the dialysis procedure may be directly related to the more common URRF: the dialyser and the membrane, microbiological quality of water and dialysate, treatment modality and online monitory equipment. The judicious selection and application of these components may collectively help improve patient outcomes in hemodialysis therapy.
Effects of dispersion in additive-pulse mode-locked lasers (1991)

The transient process of pulse shortening in a laser with a nonlinear external cavity is studied by numerical calculation. The effect of normal fiber dispersion on the steady-state output parameters is investigated. The main features of the pulse-shortening process can be understood by simple arguments. The numerical simulations indicate that pulse shortening is accompanied by an increase in the chirp of the master resonator pulse. It is shown that a chirped master resonator pulse in the presence of dispersion diminishes the pulse shortening and results in longer stationary pulse. If the chirp is strong enough, pulse shortening is even reversed into pulse lengthening. Our conclusions are supported by experimental observations.
A Scalable Heterogeneous AiP Module for a 256-Element 5G Phased Array (2023)

This paper presents design and integration considerations of a scalable 24–30 GHz 256-element phased array antenna module consisting of four 64-element tiles. We employ a heterogeneous integration approach to enable the effective and efficient integration of multiple ICs, bandpass filters, splitters, combiners, and decoupling capacitors in a multi-layered organic substrate which also integrates the 64 dual-polarized antenna array. The paper introduces and addresses technical challenges that arise in the heterogeneous integration of such large mmWave antenna-in-package (AiP) designs: 1) system architecture and functional partitioning among multiple technologies to enable performance and scalability, 2) design of the power delivery network to reduce supply modulation of mmWave active circuits, and 3) tiling considerations to preserve antenna performance when scaling to large antenna array modules. The proposed heterogeneous integration approach is validated by 360° radiation and beam scan measurements demonstrating beam scan across ±70° in E- and H- planes in both polarizations.
Efficient Transition‐Metal‐Free Oxidation of Benzylic and Secondary Alcohols to the Carbonyl Compounds Using an N‐Bromosuccinimide/NH4Cl System (2006)

The oxidation of a variety of benzylic and secondary alcohols was achieved in excellent yields using an NBS/NH4Cl system in aqueous acetonitrile (CH3CN‐H2O; 7/3 v/v) at 80°C under very mild conditions.
Separation of effects of InGaN/GaN superlattice on performance of light-emitting diodes using mid-temperature-grown GaN layer (2018)

We evaluated the electrical properties of InGaN-based light-emitting diodes (LEDs) with a superlattice (SL) layer or a mid-temperature-grown GaN (MT-GaN) layer just beneath the multiple quantum wells (MQWs). Both the SL layer and the MT-GaN layer were effective in improving the electroluminescence (EL) intensity. However, the SL layer had a more pronounced effect on the EL intensity than did the MT-GaN layer. Based on a comparison with devices with an MT-GaN layer, the overall effects of the SL could be separated into the effect of the V-pits and the structural or compositional effect of the SL. It was observed that the V-pits formed account for 30% of the improvement in the LED performance while the remaining 70% can be attributed to the structural or compositional effect of the SL.
Compact wideband rat-race hybrid utilizing composite right/left-handed transmission lines (2013)

This paper presents a compact wideband rat-race hybrid composed of composite right/left-handed transmission lines (CRLH-TLs). Using CRLH-TLs with phase delays of -90 degrees and a right-handed transmission line (RH-TL) with 90 degrees at a design frequency, a relative bandwidth of about 36% can be obtained at the design frequency of 4 GHz. Furthermore, size reduction of about 60% can be simultaneously achieved compared with a conventional rat-race hybrid utilizing only RH-TLs based on a distributed circuit theory. The validity of this design procedure has been demonstrated by em-simulations and experiments. Moreover, a trial rat-race hybrid can maintain wideband characteristics and no variation of insertion losses up to 20 dBm input power.
Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix (2017)

Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the presence and recombination of the AP synthesis gene cluster (<i>apnA-E</i>) through comparing 125 strains of the bloom-forming cyanobacterium <i>Planktothrix</i> spp., which were isolated from numerous shallow and deep water habitats in the temperate and tropical climatic zone. Ten ecologically divergent strains were purified and genome sequenced to compare their entire <i>apnA-E</i> gene cluster. In order to quantify <i>apn</i> gene distribution patterns, all the strains were investigated by PCR amplification of 2 kbp portions of the entire <i>apn</i> gene cluster without interruption. Within the 11 strains assigned to <i>P. pseudagardhii, P. mougeotii</i>, or <i>P. tepida</i> (Lineage 3), neither <i>apnA-E</i> genes nor remnants were observed. Within the <i>P. agardhii</i>/<i>P. rubescens</i> strains from shallow waters (Lineage 1, 52 strains), strains both carrying and lacking <i>apn</i> genes occurred, while among the strains lacking the <i>apnA-E</i> genes, the presence of the 5'end flanking region indicated a gene cluster deletion. Among the strains of the more derived deep water ecotype (Lineage 2, 62 strains), <i>apnA-E</i> genes were always present. A high similarity of <i>apn</i> genes of the genus <i>Planktothrix</i> when compared with strains of the genus <i>Microcystis</i> suggested its horizontal gene transfer during the speciation of <i>P. agardhii</i>/<i>P. rubescens</i>. Genetic analysis of the first (A<sub>1</sub>-) domain of the <i>apnA</i> gene, encoding synthesis of the exocyclic position of the AP molecule, revealed four genotype groups that corresponded with substrate activation. Groups of genotypes were either related to Arginine only, the coproduction of Arginine and Tyrosine or Arginine and Lysine, or even the coproduction of Arginine, Tyrosine, and Lysine in the exocyclic position of the AP-molecule. The increased structural diversity resulted from the evolution of <i>apnA</i> A<sub>1</sub> genotypes through a small number of positively selected point mutations that occurred repeatedly and independently from phylogenetic association.
Thrombogenic evaluation of two mechanical heart valve prostheses using a new in-vitro test system. (2009)

Correlation of the present in-vitro results with previously reported in-vivo results confirmed the reliability of the new system to detect local thrombogenic areas in mechanical heart valves. The new system represents a cost-effective method for optimizing the design and development of new prosthetic mechanical heart valves.
Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions (2022)

Abstract For decades, investigators have studied the interaction of Mycobacterium tuberculosis (Mtb) with macrophages, which serve as a major cellular niche for the bacilli. Because Mtb are prone to aggregation, investigators rely on varied methods to disaggregate the bacteria for these studies. Here, we examined the impact of routinely used preparation methods on bacterial cell envelop integrity, macrophage inflammatory responses, and intracellular Mtb survival. We found that both gentle sonication and filtering damaged the mycobacterial cell envelope and markedly impacted the outcome of macrophage infections. Unexpectedly, sonicated bacilli were hyperinflammatory, eliciting dramatically higher TLR2-dependent gene expression and elevated secretion of IL-1β and TNF-α. Despite evoking enhanced inflammatory responses, sonicated bacilli replicated normally in macrophages. In contrast, Mtb that had been passed through a filter induced little inflammatory response, and they were attenuated in macrophages. Previous work suggests that the mycobacterial cell envelope lipid, phthiocerol dimycocerosate (PDIM), dampens macrophage inflammatory responses to Mtb. However, we found that the impact of PDIM depended on the method used to prepare Mtb. In conclusion, widely used methodologies to disaggregate Mtb may introduce experimental artifacts in Mtb-host interaction studies, including alteration of host inflammatory signaling, intracellular bacterial survival, and interpretation of bacterial mutants.
Overexpression of a soybean salicylic acid methyltransferase gene confers resistance to soybean cyst nematode (2013)

Salicylic acid plays a critical role in activating plant defence responses after pathogen attack. Salicylic acid methyltransferase (SAMT) modulates the level of salicylic acid by converting salicylic acid to methyl salicylate. Here, we report that a SAMT gene from soybean (GmSAMT1) plays a role in soybean defence against soybean cyst nematode (Heterodera glycines Ichinohe, SCN). GmSAMT1 was identified as a candidate SCN defence-related gene in our previous analysis of soybean defence against SCN using GeneChip microarray experiments. The current study started with the isolation of the full-length cDNAs of GmSAMT1 from a SCN-resistant soybean line and from a SCN-susceptible soybean line. The two cDNAs encode proteins of identical sequences. The GmSAMT1 cDNA was expressed in Escherichia coli. Using in vitro enzyme assays, E. coli-expressed GmSAMT1 was confirmed to function as salicylic acid methyltransferase. The apparent Km value of GmSAMT1 for salicylic acid was approximately 46 μM. To determine the role of GmSAMT1 in soybean defence against SCN, transgenic hairy roots overexpressing GmSAMT1 were produced and tested for SCN resistance. Overexpression of GmSAMT1 in SCN-susceptible backgrounds significantly reduced the development of SCN, indicating that overexpression of GmSAMT1 in the transgenic hairy root system could confer resistance to SCN. Overexpression of GmSAMT1 in transgenic hairy roots was also found to affect the expression of selected genes involved in salicylic acid biosynthesis and salicylic acid signal transduction.
Study of the interplay of vaporisation, melt displacement and melt ejection mechanisms under single and multiple pulse irradiation (2006)

We report the use of a combination of profilometry, high speed imaging and recoil measurements using a ballistic pendulum to calculate the amount of material removed due to mechanisms of vaporisation, melt displacement and melt ejection when ablating aluminium with a visible nanosecond laser. Single laser pulses are shown to induce material removal predominantly by the mechanism of melt displacement at fluences <2 J.cm-2, melt displacement and vapourisation at fluences between 2 and 7 J.cm-2, and melt ejection with smaller contributions due to melt displacement and vaporisation at fluences >7 J.cm-2. Studies of the effects of multiple laser pulses, as a function of spot size and pulse rate demonstrate the additional influence of the geometric constraints of the ablation crater and cumulative heating on laser ablation.
Crystal structures of the human adiponectin receptors (2015)

Abstract Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases the activities of 5′ AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor (PPAR), respectively, thereby contributing to healthy longevity as key anti-diabetic molecules. AdipoR1 and AdipoR2 were predicted to contain seven transmembrane helices with the opposite topology to G-protein-coupled receptors. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9 and 2.4 Å resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of G-protein-coupled receptors, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may have a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the carboxy-terminal tail, of the receptors. The present information will facilitate the understanding of novel structure–function relationships and the development and optimization of AdipoR agonists for the treatment of obesity-related diseases, such as type 2 diabetes.
Modeling the Motion of Microrobots on Surfaces Using Nonsmooth Multibody Dynamics (2012)

We apply nonsmooth multibody dynamics to describe the motion of a microrobot which is driven by the wireless resonant magnetic microactuator. We first analyze the robot using a simplified analytical model, which allows us to derive characteristic and nondimensional parameters that describe its dynamics. We then perform a numerical study to analyze the nonlinearities. We predict several nonintuitive phenomena, such as switching of the direction of the velocity with changing excitation frequency, and show that both erratic and controlled motions occur under specific conditions. Our numerical results are qualitatively consistent with experimental observations and indicate that previous speculations on the motion mechanism were incorrect. The modeling method is general and readily applies to other microrobots as well.
Solvent-Free Processable and Photo-Patternable Hybrid Gate Dielectric for Flexible Top-Gate Organic Field-Effect Transistors (2017)

We report a novel solvent-free and direct photopatternable poly[(mercaptopropyl)methyl-siloxane] (PMMS) hybrid dielectric for flexible top-gate organic field-effect transistors (OFETs) utilizing a photoactivated thiol-ene reaction under UV irradiation of 254 nm to induce cross-linking, even in air and at low temperatures. In particular, a solvent-free PMMS-f dielectric film, for which an optimal cross-linking density is shown by a well-organized molar ratio between thiol and vinyl in the thiol-ene reaction, exhibited a high dielectric constant (5.4 @ 100 Hz) and a low leakage current (<1 nA mm<sup>-2</sup> @ 2 MV cm<sup>-1</sup>). The excellent dielectric characteristics of the solvent-free PMMS-hybrid dielectrics, along with their other unique characteristics of a direct photopatternability for which UV-nanoimprint lithography is used and a high surface energy of 45.6 mJ m<sup>-2</sup>, allowed the successful application of the dielectrics to flexible solvent-free top-gate OFETs with a high reliability against the radius of curvature (9.5, 7.0, and 5.5 mm) and repetitive bending cycles at the radius of curvature of 5.5 mm. This will eventually enable the proposed dielectric design to be used in a variety of applications such as flexible displays and soft organic sensors including chemical and tactile capability.
ChemInform Abstract: Nucleoside‐O‐(2‐thiono‐1,3,2‐oxathiaphospholane)S‐ Versatile Tools in the Synthesis of Oligonucleotide Analogues (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Scheduling Preventive Overtime: A New Approach for the Automotive Industry (1996)

Because over $2 billion was spent on overtime at US and Canadian automotive final assembly plants in 1994, identifying ways to reduce overtime can have a significant effect on the cost of producing vehicles. Traditionally, as described in this paper, overtime has been used to satisfy daily production quotas of finished product. But automotive assembly plants can run selected stations overtime to prepare for the next day. By adjusting the contents of the stations’ buffers at the end of the day, such ‘preventive overtime’ reduces blocking and starving tomorrow, which in turn reduces the need for overtime to meet tomorrow’s quota. The new heuristic described in this paper accommodates the practical industrial limitations of poor availability of data and minimal computational capabilities, yet makes a significant improvement over current practices.
ChemInform Abstract: NUCLEOPHILIC CHARACTER OF ALKYL RADICALS. XII. MECHANISM AND NEW SYNTHESES IN N THE OXIDATION OF ALCOHOLS BY PEROXYDISULFATE (1977)

Abstract Der Mechanismus der Oxidation von Alkoholen wie (I), (IV), (VI) und (VIII) mit K 2 S 2 O 8 in Gegenwart von protoni tem Chinolin (III) (Abfangen der radikalischen Intermediärstufen) wird untersucht.
Changes in Material Classification of the Urinary Bladder Wall After Spinal Cord Injury (2002)

Changes in the mechanical properties of the urinary bladder wall following neurogenic disease or trauma can result in bladder dysfunction. We have recently reported changes in the biaxial mechanical properties of the bladder wall 10 days after spinal cord injury in a rat model [1]. Development of a constitutive model to characterize these changes would facilitate quantitative comparisons and provide the necessary information for organ-level computational modeling. However, before an appropriate constitutive model of the bladder wall can be formulated, its material class must be identified. In the present study, we applied a generalized method for material classification of biaxial mechanical data to our previous data on the urinary bladder wall.
S0 Mode Lamb Wave Resonators Using LiNbO3 Thin Plate on Acoustic Multilayer Reflector (2013)

Lamb wave modes can be classified as a fundamental anti-symmetric mode (A 0 ), a symmetric mode (S 0 ), and their higher order modes. Membrane-type A 1 mode Lamb wave resonators have been reported by the authors for future mobile communication systems. Although the reports show promising results, it is difficult to fabricate the resonators because they have a large dispersion of phase velocity and electromechanical coupling factor, and also are fragile. In this study, the authors suggest a solidly mounted resonator (SMR)-type S 0 mode Lamb wave resonator, which can solve the above-mentioned difficulty. An SMR-type S 0 mode Lamb wave resonator was successfully realized for the first time. The resonator exhibits a 1.5 times faster phase velocity and a 1/3 smaller temperature coefficient of frequency than the commonly used surface acoustic wave (SAW) devices composed of an Al electrode and a 36–48°YX-LiTaO 3 substrate.
Inhibition of Endogenous Leukotriene-Mediated Lung Anaphylaxis in Guinea Pigs by a Novel Receptor Antagonist ONO-1078 (1990)

The inhibitory effect of ONO-1078, a novel leukotriene (LT) receptor antagonist, was investigated on guinea pig lung anaphylaxis in vitro and in vivo. It was demonstrated that this compound could inhibit the late phase of contractile responses in Schultz-Dale reactions and endogenous LT-mediated bronchoconstrictions in passively sensitized guinea pigs, in a dose-dependent fashion, implying its clinical usefulness in the treatment of human bronchial asthma.
The Effect of Tibial Tuberosity Medialization and Lateralization on Patellofemoral Joint Kinematics, Contact Mechanics, and Stability (2014)

Lateral patellofemoral joint contact pressures increased with progressive lateralization of the TT; medialization of the TT reduced these effects, restoring patellar stability, and did not cause excessive peak pressures. These data provide a rationale for medial TT transfer surgery in patients with elevated TT-TG distances.
Supplementary Figure 1 from The Dendritic Cell–like Functions of IFN-Producing Killer Dendritic Cells Reside in the CD11b<sup>+</sup> Subset and Are Licensed by Tumor Cells (2023)

Supplementary Figure 1 from The Dendritic Cell–like Functions of IFN-Producing Killer Dendritic Cells Reside in the CD11b&lt;sup&gt;+&lt;/sup&gt; Subset and Are Licensed by Tumor Cells