gebhart/patrepeval huggingface dataset:
A Single Nucleotide Deletion in an ABC Transporter Gene Leads to a Dwarf Phenotype in Watermelon (2019)

Dwarf habit is one of the most important traits in crop plant architecture, as it can increase plant density and improved land utilization, especially for protected cultivation, as well as increasing lodging resistance and economic yield. At least four dwarf genes have been identified in watermelon, but none of them has been cloned. In the current study, the <i>Cldw-1</i> gene was primary-mapped onto watermelon chromosome 9 by next-generation sequencing-aided bulked-segregant analysis (BSA-seq) of F<sub>2</sub> plants derived from a cross between a normal-height line, WT4, and a dwarf line, WM102, in watermelon. The candidate region identified by BSA-seq was subsequently validated and confirmed by linkage analysis using 30 simple sequence repeat (SSR) markers in an F<sub>2</sub> population of 124 plants. The <i>Cldw-1</i> gene was further fine-mapped by chromosome walking in a large F<sub>2</sub> population of 1,053 plants and was delimited into a candidate region of 107.00 kb. Six genes were predicted to be in the candidate region, and only one gene, <i>Cla010337</i>, was identified to have two single nucleotide polymorphisms (SNPs) and a single nucleotide deletion in the exons in the dwarf line, WM102. A derived cleaved amplified polymorphic sequence (dCAPS) marker was developed from the single nucleotide deletion, co-segregated with the dwarf trait in both the F<sub>2</sub> population and a germplasm collection of 165 accessions. <i>Cla010337</i> encoded an ATP-binding cassette transporter (ABC transporter) protein, and the expression levels of <i>Cla010337</i> were significantly reduced in all the tissues tested in the dwarf line, WM102. The results of this study will be useful in achieving a better understanding of the molecular mechanism of the dwarf plant trait in watermelon and for the development of marker-assisted selection (MAS) for new dwarf cultivars.
Complete coding regions of the prototypes enterovirus B93 and C95: Phylogenetic analyses of the P1 and P3 regions of EV‐B and EV‐C strains (2014)

Complete coding regions were sequenced for two new enterovirus genomes: EV-B93 previously identified by VP1 sequencing, derived from a child with acute flaccid paralysis in the Democratic Republic of Congo; and EV-C95 from a French soldier with acute gastroenteritis in Djibouti. The EV-B93 P1 had more than 30% nucleotide divergence from other EV-B types, with highest similarity to E-15 and EV-B80. The P1 nucleotide sequence of EV-C95 was most similar, 71%, to CV-A21. Complete coding regions for the new enteroviruses were compared with those of 135 EV-B and 176 EV-C strains representing all types available in GenBank. When strains from the same outbreak or strains isolated during the same year in the same geographical region were excluded, 27 of the 58 EV-B, and 16 of the 23 EV-C types were represented by more than one sequence. However, for EV-B the P3 sequences formed three clades mainly according to origin or time of isolation, irrespective of type, while for EV-C the P3 sequences segregated mainly according to disease manifestation, with most strains causing paralysis, including polioviruses, forming one clade, and strains causing respiratory illness forming another. There was no intermixing of types between these two clades, apart from two EV-C96 strains. The EV-B P3 sequences had lower inter-clade and higher intra-clade variability as compared to the EV-C sequences, which may explain why inter-clade recombinations are more frequent in EV-B. Further analysis of more isolates may shed light on the role of recombinations in the evolution of EV-B in geographical context.
Reduction and loss of the iron center in the reaction of the small subunit of mouse ribonucleotide reductase with hydroxyurea (1993)

Ribonucleotide reductase is a key enzyme for DNA synthesis in living cells, and the mechanisms for its reactions with inhibitors are of interest because the inhibitors are potential antiproliferative agents. Protein R2, the small subunit of mouse ribonucleotide reductase, contains a pair of mu-oxo-bridged ferric ions and a tyrosyl free radical in each of its two polypeptide chains. Light absorption spectroscopy was used to probe the reactions of these redox centers with hydroxyurea (HU), a potent inhibitor of iron containing ribonucleotide reductases. In Escherichia coli protein R2, HU reacts with the tyrosyl radical without affecting the iron center. In contrast to the case for the E. coli protein, HU destroys the specific absorbance bands of both the iron center and the radical on a similar time scale in mouse protein R2, and this is accompanied by release of iron from the protein. Anaerobic experiments with the iron chelator bathophenanthroline present during the HU reaction indicate that the iron is released from the mouse R2 protein in the ferrous form after treatment with HU. The reduced iron center, formed by reaction of Fe2+ with mouse apoprotein R2 under anaerobic conditions, was found to be much less stable than the native Fe3+ site in the presence of suitable iron chelators. The observations are of importance for understanding the mode of action of HU on mammalian cells and for the general question of the stability of the iron center of mouse protein R2 in different redox states.
Integrated Common-Mode Filter for GaN Power Module With Improved High-Frequency EMI Performance (2023)

While the employment of wide bandgap (WBG) devices in high-frequency and high-voltage applications brings benefits such as reduced system size and improved efficiency, it aggravates the electromagnetic interference (EMI) issue due to fast switching. High-frequency EMI noise suppression relies mainly on the filter design, where the filter's performance is strongly affected by parasitics. Through analyzing the common-mode (CM) equivalent circuit of a half-bridge power module, this letter identifies the key parasitics that dominate the performance of a common-mode filter (CMF) at high frequencies. To minimize the parasitics, the concept of integrating the CMF inside the WBG power module package is developed to improve the noise attenuation. A π-type CMF is integrated with a half-bridge GaN-based power module as a prototype to validate the concept. Experiments are conducted by measuring the CM noise spectrum received by the line impedance stabilization networks (LISNs) from the hard switching of the designed power module under 70 V and 80 kHz. Comparing the measured results of the integrated CMF to the externally added CMF, up to 50 dBμV more attenuation is achieved by the integrated CMF in the frequency range of 10 to 100 MHz, verifying the theoretical analysis and the established CM equivalent circuit.
Fluorometry of ischemia reperfusion injury in rat lungsin vivo (2013)

Previously we demonstrated the utility of optical fluorometry to evaluate lung tissue mitochondrial redox state in isolated perfused rats lungs under various chemically-induced respiratory states. The objective of this study was to evaluate the effect of acute ischemia on lung tissue mitochondrial redox state in vivo using optical fluorometry. Under ischemic conditions, insufficient oxygen supply to the mitochondrial chain should reduce the mitochondrial redox state calculated from the ratio of the auto-fluorescent mitochondrial metabolic coenzymes NADH (Nicotinamide Adenine Dinucleotide) and FAD (Flavoprotein Adenine Dinucleotide). The chest of anesthetized, and mechanically ventilated Sprague-Dawley rat was opened to induce acute ischemia by clamping the left hilum to block both blood flow and ventilation to one lung for approximately 10 minutes. NADH and FAD fluorescent signals were recorded continuously in a dark room via a fluorometer probe placed on the pleural surface of the left lung. Acute ischemia caused a decrease in FAD and an increase in NADH, which resulted in an increase in the mitochondrial redox ratio (RR=NADH/FAD). Restoration of blood flow and ventilation by unclamping the left hilum returned the RR back to its baseline. These results (increase in RR under ischemia) show promise for the fluorometer to be used in a clinical setting for evaluating the effect of pulmonary ischemia-reperfusion on lung tissue mitochondrial redox state in real time.
Formation of Well‐Organized Self‐Assembled Films from Peptide Nanotubes (2007)

A method for constructing peptide-nanotube-based films is demonstrated. A centimeter-sized film of diphenylalanine is successfully formed. The formation process includes the dissociation of nanotubes in a polar cosolvent solution and their recrystallization in spherulitic form on solid substrates, while preserving the basic crystallographic structure of the nanotubes (see figure and cover). In addition, silver-embedded peptide nanotube composite networks are created.
Evoked Potentials in the Hippocampus and Learning (1989)

The hippocampus is a large forebrain structure that contains the major components of primitive cortex. Hippocampal cellular elements receive inputs from, and send outputs to, important areas of the brain stem (hypothalamus) and neocortex (entorhinal cortex). The exact nature of the functions subserved by the hippocampus in the mammalian brain has eluded neuroscientists for at least two decades. In recent years, however, major strides have been made in our understanding of the behavioral functions of the hippocampus. A new and emerging set of observations suggests that hippocampal electrical events bear a relationship to cognitive and perceptual factors, on the one hand, and conditioning and learning processes, on the other. These findings indicate that one of the main functions of this structure is to process sensory information relevant to both the behavioral and environmental context in which the animal exists at any one point in time.
Small rodents as reservoirs of Cryptosporidium spp. and Giardia spp. in south-western Poland (2015)

[i]Cryptosporidium[/i] spp. and [i]Giardia[/i] spp. have been detected in a range of host species, including rodents. The aim of this study was to determine the distribution of these pathogens and recognition of the reservoir role of rodents in the maintenance of these pathogens in south-western Poland. Additionally, preliminary molecular studies were conducted to elucidate the species and genotypes of [i]Cryptosporidium[/i] and [i]Giardia[/i] identified in this study. Stool samples (n=266) from [i]A. agrarius[/i],[i] A. flavicollis[/i] and [i]M. glareolus[/i], were subjected for analyses. Values of prevalence were 61.7, 68.3 and 68.1%, respectively, for [i]Cryptosporidium[/i] spp. and 41.7, 24.4 and 38.4%, respectively, for [i]Giardia[/i] spp. There was a statistically significant correlation between host species and [i]Giardia[/i] infection where[i] A. agrarius[/i] was the species of the highest prevalence. Statistically significant differences were not found for comparisons made for study sites and occurrence of [i]Giardia[/i] spp. and [i]Cryptosporidium[/i] spp. Due to preliminary nested PCR results, specific amplifications of [i]Cryptosporidium[/i] COWP and SSU rRNA genes were obtained for several isolates taken from rodent host species. One isolate recovered from [i]A. agrarius[/i] (from a semi-aquatic, urban area) was identified as [i]C. parvum[/i] and revealed 100% similarity with sequences obtained from humans. To the best of the knowledge of the authors, this is the first record of the [i]C. parvum[/i] zoonotic species from the striped field mouse. Also recorded were the first findings of [i]C. ubiquitum[/i] from three small rodent species.
On classification of environmental acoustic data using crowds (2017)

In this work, we use crowds for acoustic classification of animal species in supervised and unsupervised manners. We demonstrate the effectiveness of the proposed triplet based crowdsourcing systems via actual experiments. Moreover, we propose a generalized 1-bit RPCA algorithm to further improve classification performance. The unique marriage of crowdsourcing and generalized 1-bit RPCA algorithm is shown to yield excellent performance for acoustic data classification.
X-Ray crystal structures of 2,2′-bridged biphenyls with heterocyclic bridging rings: contraction in ring size on reduction (1988)

X-Ray crystal structure analysis confirms that two of the four tetrabenzo [b,d,h,j][1,6]diazacyclododecines previously investigated have 12-membered rings; there is a strong presumption that the other two have a similar structure. Three of the four compounds undergo (dimethylamino)borane reduction to the tetrahydro derivatives in a process shown by X-Ray analysis and/or n.m.r. spectroscopy to involve C–N bond breaking and ring contraction from 12- to seven-membered rings. The fourth compound is shown by X-ray analysis to retain its (presumed) 12-membered ring structure when the tetrahydro derivative is produced by catalytic hydrogenation.
Femtosecond Technology in Japan (1998)

The aim of this study was to determine the enhancement of Scirpus triqueter in the dissipation of pyrene and the interaction of pyrene with plant, soil enzymes and microbial community. The results indicated that the dissipation ratios of pyrene in the rhizospheric and non-rhizospheric soil were 64.65 ± 3.86% and 54.49 ± 2.74%, respectively, and were higher than that in the unplanted soil (42.60 ± 0.71%) at 80 d after planting S. triqueter. The pyrene was toxic to S. triqueter, as evidenced by growth inhibition in height, diameter, shoot number and biomass during the planting period. The activities of dehydrogenase decreased significantly at the presence of pyrene in soils, and increased remarkably with the introduction of S. triqueter. It was found that the pyrene addition increased the ratios of fungal/total fatty acids and gram-positive/gram-negative, but the presence of S. triqueter decreased the ratios of gram-positive/gram-negative. A larger stress level was found in the pyrene treated soils without S. triqueter. The ratio of aerobic/anaerobic bacteria decreased with increasing pyrene concentration, but increased when S. triqueter was planted. The principal analysis of phospholipid fatty acid signatures revealed that microbial community structures in the rhizospheric and non-rhizospheric soil were similar, but different from those in the unplanted and control soil.
Highly Enantio‐ and Diastereoselective Organocatalytic Asymmetric Domino Michael–Aldol Reaction of β‐Ketoesters and α,β‐Unsaturated Ketones (2004)

Drei oder vier benachbarte stereogene Zentren werden durch die Titelreaktion gezielt aufgebaut (siehe Schema). Man erhält bei ausgezeichneten Enantioselektivitäten (bis 99 % ee) jeweils nur ein Diastereomer der optisch aktiven Cyclohexanone, die in wertvolle Synthesebausteine umgewandelt werden können. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2004/z53364_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Relationship between protein/solvent proton exchange and progressive conformation and fluctuation changes in hemoglobin (1990)

The pH dependence of the tertiary structural changes and the quaternary reorganization of the alpha beta interface of oxyhemoglobin in solution has been previously observed in our laboratory. The present work aims to establish whether or not these progressive structural changes with pH result from proton exchange between the protein and the solvent. We therefore have used infrared spectroscopy, acid/base titration and 1H/2H exchange to assess the effect of external proton concentration on the structural and dynamic properties of the hemoglobin molecule in solution. This study is also performed on the carbonmonoxy form since the affinity of hemoglobin for CO is much higher than for oxygen. The present findings demonstrate that affinity changes are closely related to protein fluctuations, as well as structural modifications. An increased affinity, induced either by ligand replacement or pH variation, is associated with the constrained chains exhibiting a lower degree of fluctuation, together with a looser alpha beta interface association.
Intracellular antibodies: a revolution waiting to happen? (2006)

Antibodies and their derivatives play a key role in modern drug development, as both research tools and therapeutic entities in their own right. The combination of high-affinity binding and exquisite specificity makes them ideal agents for controlled intervention in biological processes. Evolution has designed antibodies to function in the circulation and interstitial spaces of a tissue or organism, but many potentially valuable drug targets are intracellular and therefore beyond the reach of standard antibodies. Some of the recent advances and current pitfalls in attempts to adapt antibodies for intracellular use are described, and the ultimate potential of this powerful but underused technology is discussed.
Monitoring in a Virtualized Environment (2010)

Monitoring solutions for virtualized infrastructure (VI) should evolve to collect, analyze and provide configuration recommendation based on a broader range of operational metrics.A virtualized infrastructure is a complex interaction of hardware (servers, network and storage), hosting variety of multi-tier application with specific service level requirements and governed by their security and compliance policies.Most existing solutions of today monitor and analyze only a subset of these interactions.The analysis and recommendation obtained tend to optimize only particular aspects of the infrastructure and can potentially introduce violations for the others.A virtualized infrastructure is dynamic in nature, providing immense opportunities to automate configuration changes to virtual machines, networks and storage.It delivers the capability to administer the whole of infrastructure as a large resource pool shared by multiple workloads.Monitoring solutions that look at only few aspects end up forcing administrators to create silos within the infrastructure that are specially designed to ensure that business service requirements are met for the specific applications running there.A monitoring solution that can collect and analyze multiple aspects for assisting in decision making and process automation can deliver greater efficiency to the virtualized infrastructure.In this paper we argue the importance of having a monitoring solution that provides a holistic view of the virtualized infrastructure.We discuss the need for solutions to be capable of monitoring and analyzing a broader set of metrics such as health of infrastructure components; performance of operating environment such as hypervisors, operating systems and application running on them; capacity utilization indicators for server, networks and storages; information available with configuration and change management database containing policies including security and compliance policies.We also take a look at what these broader set of metrics are and who would be interested in them.The paper further proposes a monitoring framework for collecting and analyzing the above mentioned aspects of a virtual infrastructure to develop a more complete solution.
Discharge-driven 46.9-nm amplifier with gain-length approaching saturation (1995)

Gain length products up to gl/spl ap/14 for the J=0-1 line of Ne-like Ar at 46.9 nm have been achieved in 15-cm-long plasma columns generated by a fast capillary discharge. Amplification in plasma columns up to 20 cm in length was investigated. The laser line intensity is observed to increase exponentially for plasma lengths of up to 15 cm, above which it is observed to saturate. The saturation behavior is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Simple Method for the Investigation of Cell Separation Effects of Blood With Physiological Hematocrit Values (2014)

Even though the separation of blood into erythrocyte-rich and erythrocyte-poor areas is well known in physiological setups such as small vessels, it has recently come into focus in small gaps in cardiovascular applications. Studies show that separation effects occur, for example, in gaps in hydrodynamic bearings, where they can have a positive effect on hemolysis. Separation effects depend on the hematocrit value, but due to visualization issues, studies in small gaps used very low hematocrit values. In this study, a test setup and an evaluation method for the investigation of separation effects of blood with hematocrit values of 30, 45, and 60% were developed. The erythrocyte distribution was evaluated by means of gray scale value distribution. This principle is based on the fact that an erythrocyte-rich region is more opaque than an erythrocyte-poor region. The experimental setup is designed in a way that no further processes (e.g., fluorescence labeling) need to be carried out which might change the properties of the membrane of the erythrocytes, and therefore their flow properties. Additionally, the method is executable with basic laboratory equipment, which makes it applicable for many laboratories. To validate the feasibility of the method, the influence of the diameter and the flow rate on the migration of erythrocytes were studied in micro channels for three different physiological hematocrit values. Even though no individual cells were traced, plasma layer and areas of high erythrocyte concentration could be identified. Dependencies of the erythrocyte distribution on flow rate and channel diameter were validated. The influence of the hematocrit value was demonstrated as well and showed the hematocrit value to be a crucial factor when investigating cell separation. The experimental results were consistent with findings in the literature. As the developed method is suitable for physiological hematocrit values and easy to handle, it provides an optimal basis for cell separation studies in gap models with whole blood, for example, hydrodynamic bearings, where it can be used to optimize these devices.
Polysulfides as biologically active ingredients of garlic (2007)

Garlic has long been considered as a natural remedy against a range of human illnesses, including various bacterial, viral and fungal infections. This kind of antibiotic activity of garlic has mostly been associated with the thiosulfinate allicin. Even so, recent studies have pointed towards a significant biological activity of trisulfides and tetrasulfides found in various Allium species, including a wide range of antibiotic properties and the ability of polysulfides to cause the death of certain cancer cells. The chemistry underlying the biological activity of these polysulfides is currently emerging. It seems to include a combination of several distinct transformations, such as oxidation reactions, superoxide radical and peroxide generation, decomposition with release of highly electrophilic S(x) species, inhibition of metalloenzymes, disturbance of metal homeostasis and membrane integrity and interference with different cellular signalling pathways. Further research in this area is required to provide a better understanding of polysulfide reactions within a biochemical context. This knowledge may ultimately form the basis for the development of 'green' antibiotics, fungicides and possibly anticancer agents with dramatically reduced side effects in humans.