gebhart/patrepeval huggingface dataset:
2-Hydroxypropyl-β-Cyclodextrin Removes All- Trans Retinol from Frog Rod Photoreceptors in a Concentration-Dependent Manner (2010)

The effectiveness of HP-beta-CD shows that a specialized interaction with the cell membrane is not necessary for the efficient transfer of all-trans retinol between the cell membrane and the carrier. The transfer occurs through a collision-based mechanism, as indicated by the linear increase of the rate of removal with the carrier concentration.
Development and Field Testing of Advanced Ceramic Proppants (2013)

Abstract A unique family of advanced ceramic proppants has been developed based on formulated mixed-metal oxides. In contrast to conventional top-down ceramic proppant manufacturing, a bottom-up process is used to coat ceramic cores with highly-engineered layers of mixed-metal oxide. This process yields a very strong, light proppant with well-controlled porosity, and a narrow size distribution. Laboratory results show that individual advanced ceramic proppant beads are much stronger than conventional ceramic proppant grains, and that the strength distribution is also much tighter than conventional ceramic proppants. The strength profile of the engineered beads bears a close relationship to the generation of conductivity-damaging crush fines. As a result, the conductivity measured in industry-standard tests is as much as 40% higher than that of conventional ceramic proppants, and this improvement is maintained over a wide range of closure stresses and multiple stress cycles. There is thus a critical link between individual proppant bead behavior and overall proppant pack performance. Proppant transport in slickwater is a result of three major mechanisms: gravity settling (Stokes Law), sedimentation (dune formation), and saltation. The low density of advanced ceramic proppants reduces the settling rate, and the low coefficient of friction reduces the height of dunes, resulting in proppant transport further into the fracture. An important new property related to proppant transport in slickwater has been identified, i.e., the coefficient of restitution. A high coefficient of restitution reduces clustered settling, and results in more active saltation. A new laboratory test to compare the coefficient of restitution of different proppants has been developed. In this test, advanced ceramic proppant beads typically move approximately 40% further than conventional ceramic particles, and twice as far as sand. A comprehensive field test of Advanced Ceramic Proppants was performed in the Permian Basin. Ten pairs of wells were selected and the new material was pumped into one member of each pair, while conventional ceramic proppant was used in the other. Advanced Ceramic Proppant increased cumulative 12-month oil production by 20% compared to the offset wells. The statistical techniques which demonstrate this improvement also identified some key variables which impacted production, including stimulation treatment execution and interference effects. The use of Advanced Ceramic Proppant increased the NPV of the wells by 25% relative to conventional ceramic proppant, and the incremental cost of the treatment was paid back in 3 to 4 months.
Drugs for glaucoma (2002)

Older drugs for glaucoma reduce intra-ocular pressure, but often have unpleasant adverse effects. They still have a role in therapy, but there are now newer drugs which overcome some of the problems. The topical carbonic anhydrase inhibitors decrease the secretion of aqueous humour, while lipid-receptor agonists increase uveoscleral outflow. Alpha 2 agonists use both mechanisms to reduce intra-ocular pressure. If a patient needs more than one drug to control their glaucoma, the new drugs generally have an additive effect when used in combination regimens.
15N−15N J-Coupling Across HgII:  Direct Observation of HgII-Mediated T−T Base Pairs in a DNA Duplex (2006)

N−N J-coupling across a metal center (2JNN) was clearly detected in a biological macromolecule (DNA duplex) for the first time. By using 2JNN, the base pairing mode of mercury-mediated T−T pairs (T−HgII−T) was definitely determined. This pairing mode was found to be a novel metal ion-binding mode for DNA and RNA molecules, in which imino proton−metal exchange processes are included. Accordingly, 2JNN is highly important for the determination of the chemical structures of metal-mediated base pairs.
A nomenclature for avian coronavirus isolates and the question of species status (2001)

Abstract Currently, there is no agreed naming system for isolates of infectious bronchitis virus (IBV), whose host is the domestic fowl (Gallus gallus domesticus). A uniform, informative system for naming IBV isolates would be very helpful. Furthermore, the desirability of a single naming system has become more important with the recent discoveries that coronaviruses with genome organizations and gene sequences very similar to those of IBV have been isolated from turkeys (Meleagris gallopavo) and pheasants (Phasianus colchicus). To date, no genetic features have been found that are unique to turkey isolates and to pheasant isolates that would permit unequivocal differentiation from IBVs. Should the avian coronaviruses from turkeys, pheasants and other birds each be considered as distinct coronavirus species? Or should avian coronaviruses that have gene sequences similar to those of IBV be treated as host-range variants of IBV or, more objectively, as host-range variants of a species that might be called avian coronavirus (ACoV)? Clearly, the topic of avian coronavirus species differentiation requires debate. For the moment, a naming system for avian coronavirus isolates is overdue. Increasingly, papers will include data of coronaviruses isolated from more than one species of bird. It is desirable to have a nomenclature for avian coronaviruses that indicates the host species of origin. Furthermore, it would be helpful if the name of an isolate included the country/region of origin, an isolate number and the year of isolation. The names of avian paramyxovirus (APMV) and avian influenza virus (AIV) isolates have long since contained this information; I suggest that we adopt a similar convention for isolates of avian coronaviruses. For example, the D274 isolate of IBV could be named chicken/Netherlands/D274/78. Representatives of avian coronaviruses from turkey and pheasant would include turkey/United States(Nc)/NC95/95 and pheasant/UK/750/83. Two upper case letters would be used to denote country of isolation, whereas one upper and one lower case letter would be used to indicate state or province, e.g. Nc, North Carolina. The full-length names could be abbreviated, when desired, similar to the convention used for AIV isolates, e.g. chNL78, tyUS(Nc)95 and phUK83. If the serotype of an isolate has been clearly established, this might be included in the name at end, like the serotype designation of AIVs, e.g. chicken/China/NRZ/91 (Mass.) for the Chinese isolate of the Massachusetts serotype. This suggested naming system for isolates is essentially neutral with regard to whether viruses from different bird species should be considered as different coronavirus species or simply as variants of just one avian coronavirus species. In my opinion an informative nomenclature for avian coronavirus isolates is required now, to improve communication, and need not be delayed until a decision on the definition of coronavirus species has been made.
Unique coexpression in osteoblasts of broadly expressed genes accounts for the spatial restriction of ECM mineralization to bone (2005)

Extracellular matrix (ECM) mineralization is a physiological process in bone and a pathological one in soft tissues. The mechanisms determining the spatial restriction of ECM mineralization to bone physiologically are poorly understood. Here we show that a normal extracellular phosphate concentration is required for bone mineralization, while lowering this concentration prevents mineralization of any ECM. However, simply raising extracellular phosphate concentration is not sufficient to induce pathological mineralization, this is because of the presence in all ECMs of pyrophosphate, an inhibitor of mineralization. ECM mineralization occurs only in bone because of the exclusive coexpression in osteoblasts of Type I collagen and Tnap, an enzyme that cleaves pyrophosphate. This dual requirement explains why Tnap ectopic expression in cells producing fibrillar collagen is sufficient to induce pathological mineralization. This study reveals that coexpression in osteoblasts of otherwise broadly expressed genes is necessary and sufficient to induce bone mineralization and provides evidence that pathological mineralization can be prevented by modulating extracellular phosphate concentration.
Hemodynamic alterations in left ventricular function consequent to ventricular pacing (1965)

Mongrel dogs were used to quantify left ventricular function (LVF) in response to subendocardial electrical pacing from three left ventricular sites and one right ventricular site (RVO). Ventricular pacing sites were compared with atrial pacing at constant heart rates. LVF was significantly diminished with ventricular pacing when left ventricular pressure, maximal rate of left ventricular pressure rise, cardiac output, stroke work, and stroke power were considered. Left ventricular pacing values were significantly greater than RVO pacing values. Developed tension (DT) and maximal rate of tension development (max. dT/dt) were recorded from a strain-gauge arch; max. dT/dt decreased disproportionately greater than the decrease in DT with ventricular pacing. The reduced LVF was shown to be independent of myocardial contractility, heart rate, end-diastolic fiber length, previous tension, and resistance to shortening. Temporal dyssynergy of left ventricular contraction was shown to be an important determinant of LVF in addition to the above variables. Left ventricular synergism must be taken into account when assessing myocardial contractility in the intact left ventricle.
Thwarting the power-hungry disk (1994)

Minimizing power consumption is important for mobile computers, and disks consume a significant portion of system-wide power. There is a large difference in power consumption between a disk that is spinning and one that is not, so systems try to keep the disk spinning only when it must. The system must trade off between the power that can be saved by spinning the disk down quickly after each access and the impact on response time from spinning it up again too often. We use trace-driven simulation to examine these trade-offs, and compare a number of different algorithms for controlling disk spin-down. We simulate disk accesses from a mobile computer (a Macintosh Powerbook Duo 230) and also from a desktop workstation (a Hewlett-Packard 9000/845 personal workstation running HP-UX), running on two disks used on mobile computers, the Hewlett-Packard Kittyhawk C3014A and the Quantum GofflDrive 120. We show that the &amp;quot;perfect&amp;quot; off-line algorithm---one that consumes minimum power without increa...
Shaded rendering and shadow computation for polyhedral animation (1990)

The present study aimed to investigate the association between drug resistance and class I, II and III integrons in <i>Acinetobacter baumannii</i> (ABA). Multilocus sequence typing (MLST) is a tool used to analyze the homology among house-keeping gene clusters in ABA and ABA prevalence and further provides a theoretical basis for hospitals to control ABA infections. A total of 96 clinical isolates of non-repeating ABA were harvested, including 74 carbapenem-resistant ABA (CRABA) and 22 non-CRABA strains, and used for bacterial identification and drug susceptibility analysis. Variable regions were sequenced and analyzed. Then, 7 pairs of housekeeping genes were amplified and sequenced via MLST and sequence alignment was performed against the Pub MLST database to determine sequence types (STs) strains and construct different genotypic evolutionary diagrams. The detection rate of CRABA class I integrons was 13.51% (10/74); no class II and III integrons were detected. However, class I, II and III integrons were not detected in non-CRABA strains. The variable regions of 9 of 10 class I integrons were amplified and 10 gene cassettes including aacC1, aac1, aadDA1, aadA1a, aacA4, dfrA17, aadA5, aadA1, aadA22 and aadA23 were associated with drug resistance. The 96 ABA strains were divided into 21 STs: 74 CRABA strains containing 9 STs, primarily ST208 and ST1145 and 22 non-CRABA strains containing 18 STs, primarily ST1145. Class I integrons are a critical factor underlying drug resistance in ABA. CRABA and non-CRABA strains differ significantly; the former primarily contained ST208 and ST1145, and the latter contained ST1145. Most STs were concentrated in intensive care units (ICUs) and the department of Neurology, with the patients from the ICUs being the most susceptible to bacterial infection. In the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, ABA is potentially horizontally transmitted and MLST can be used for clinical ABA genotyping.
RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding (2014)

RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.
Validation of a simple model for predicting liver fibrosis in HIV/hepatitis C virus‐coinfected patients (2005)

A simple model incorporating readily available laboratory data is highly predictive of significant fibrosis in HIV/HCV coinfection and could serve as a biopsy-sparing measure, thus making treatment more accessible for this population.
Large scale learning to rank (2009)

Pairwise learning to rank methods such as RankSVM give good performance, but suffer from the computational burden of optimizing an objective defined over O(n 2) possible pairs for data sets with n examples. In this paper, we remove this super-linear dependence on training set size by sampling pairs from an implicit pairwise expansion and applying efficient stochastic gradient descent learners for approximate SVMs. Results show orders-of-magnitude reduction in training time with no observable loss in ranking performance. Source code is freely available at:
Optimization of Replication, Transcription, and Translation in a Semi-Synthetic Organism (2019)

Previously, we reported the creation of a semi-synthetic organism (SSO) that stores and retrieves increased information by virtue of stably maintaining an unnatural base pair (UBP) in its DNA, transcribing the corresponding unnatural nucleotides into the codons and anticodons of mRNAs and tRNAs, and then using them to produce proteins containing noncanonical amino acids (ncAAs). Here we report a systematic extension of the effort to optimize the SSO by exploring a variety of deoxy- and ribonucleotide analogues. Importantly, this includes the first in vivo structure-activity relationship (SAR) analysis of unnatural ribonucleoside triphosphates. Similarities and differences between how DNA and RNA polymerases recognize the unnatural nucleotides were observed, and remarkably, we found that a wide variety of unnatural ribonucleotides can be efficiently transcribed into RNA and then productively and selectively paired at the ribosome to mediate the synthesis of proteins with ncAAs. The results extend previous studies, demonstrating that nucleotides bearing no significant structural or functional homology to the natural nucleotides can be efficiently and selectively paired during replication, to include each step of the entire process of information storage and retrieval. From a practical perspective, the results identify the most optimal UBP for replication and transcription, as well as the most optimal unnatural ribonucleoside triphosphates for transcription and translation. The optimized SSO is now, for the first time, able to efficiently produce proteins containing multiple, proximal ncAAs.
Variations in the formation of thoracic splanchnic nerves (2014)

The thoracic splanchnic nerves and celiac ganglia play a major role in pain management of upper abdominal disorders, particularly chronic pancreatitis and pancreatic cancer. The variable anatomy of the splanchnic nerves is becoming increasingly important in view of the splanchnicectomy being used more often for relief of pain originating from the upper abdominal viscera. In the present study variations of the roots of origin, formation and course of the splanchnic nerves were observed by using gross dissections of eighty-eight sides of thirty-four adult and ten foetal cadavers. The greater splanchnic nerve was found on both sides of all the adult cadavers as well as foetal specimens (100%). The lesser splanchnic nerve was found in 95.45% (84 sides) of the sides. The lesser splanchnic nerve was found to be absent unilaterally in four adult cadavers (two each of right and left sides). The least splanchnic nerve was found in 67.5% of the sides. Excepting a right side of one adult female cadaver and a left side of a male cadaver, where the highest root of the greater splanchnic nerve originated from T3, in all other cases the highest root of the greater splanchnic nerve originated from T4 ganglion onwards. The greater splanchnic nerve was formed by two or more roots. A maximum number of seven roots was found in three sides of adult female cadavers (3.4%). In a large number of instances (54 cases - 64.28%) the lesser splanchnic nerve was formed by a single root. Awareness and appreciation of the variant patterns of the splanchnic nerves is of great importance to the surgeon undertaking thoracic splanchnicectomy, since this technique has been demonstrated to be of tremendous potential in pain abolition or control because of its simplicity and absence of any morbidity and potential mortality associated with thoracotomy.
Ehlers-Danlos syndrome type VIIB. Morphology of type I collagen fibrils formed in vivo and in vitro is determined by the conformation of the retained N-propeptide (1993)

Previously we showed that fibrils generated from collagen and pNcollagen-ex6 from fibroblasts of an individual with Ehlers-Danlos syndrome (EDS) type VIIB were hieroglyphic in cross-section and all N-propeptides were located at the fibril surface. Hieroglyphs were resolved to near-cylindrical fibrils (that were similar in appearance to the fibrils seen in the tissues of individuals with EDS type VIIB) by treatment with N-proteinase which cleaved the pN alpha 1(I) chains but not the pN alpha 2(I)-ex6 chains (Watson, R. B., Wallis, G. A., Holmes, D. F., Viljoen, D., Byers, P. H., and Kadler, K. E. (1992) J. Biol. Chem. 267, 9093-9100). Here, quantitative scanning transmission electron microscopy (STEM) showed that N-propeptides in hieroglyphs were in a "bent-back" conformation and thus located exclusively in the overlap zone of the fibril D-period (D = 67 nm). In contrast, STEM of fibrils from the dermis of an individual with EDS type VIIB showed that partially cleaved N-propeptides (in which cleaved pN alpha 1(I) remained in noncovalent association with pN alpha 2(I)-ex6 chains) were distributed equally between the gap and overlap zones of the fibrils. Comparison of experimental data with theoretical mass distributions of the fibril based on amino acid sequence data gave a consistent value of 33 nm for the total axial extent for the N-propeptides in hieroglyphic and tissue fibrils irrespective of the location of N-propeptides to the gap or overlap zone. These data exclude the possibility that N-propeptides adopt a random configuration, but rather, that they locate to specific sites in the gap and overlap zones. The results demonstrated that cleavage of pN alpha 1(I) chains in vivo releases the N-propeptides from the constraints of the bent-back conformation. Co-distribution of partially cleaved N-propeptides between gap and overlap zones allows a higher surface packing density of N-propeptides and explains how circularity of large diameter fibrils can be achieved despite the retention of N-propeptides in tissues of individuals with EDS type VIIB.
An Assessment of the Anaerobic Vial of Paired NR 6A and NR 7N Bactec Blood Cultures (1993)

Clinical laboratories should carefully examine the use of the routine anaerobic blood culture and consider its replacement with larger volume aerobic blood culture vials.
Random, Ephemeral Transaction Identifiers in dynamic sensor networks (2002)

Recent advances in miniaturization and low-cost, low-power design have led to active research in large-scale, highly distributed systems of small, wireless, low-power unattended sensors and actuators. We explore the use of Random, Ephemeral TRansaction Identifiers (RETRI) in such systems, and contrast it with the typical design philosophy of using static identifiers in roles such as node addressing or efficient data naming. Instead of using statically assigned identifiers that are guaranteed to be unique, nodes randomly select probabilistically unique identifiers for each new transaction. We show how this randomized scheme can significantly improve the system's energy efficiency in contexts where that efficiency is paramount, such as energy-constrained wireless sensor networks. Benefits are realized if the typical data size is small compared to the size of an identifier, and the number of transactions seen by an individual node is small compared to the number of nodes that exist in the entire system. Our scheme is designed to scale well: identifier sizes grow with a system's density not its overall size. We quantify these benefits using an analytic model that predicts our scheme's efficiency. We also describe an implementation as applied to packet fragmentation and an experiment that validates our model.
Synthesis of Planar-Chiral Paracyclophanes via Samarium(II)-Catalyzed Intramolecular Pinacol Coupling (2005)

[reaction: see text] A series of [n]paracyclophanediols (n = 8-12) was synthesized by samarium-catalyzed pinacol coupling for their ansa-bridge formation. Enantiomerically pure [n]paracyclophane esters were derived from the diols in a several steps via chiral resolution (for n = 10) or via crystallization-induced asymmetric transformation (for n = 11) by using amino alcohol auxiliaries and their selective cleavages.
Chaos communications-principles, schemes, and system analysis (2002)

This paper provides a comprehensive overview of chaotic communication methods and schemes with emphasis on digital schemes. Starting from general demands for communications, the general communication system structure is introduced. From this basic viewpoint, different classical and chaotic modulation and demodulation methods are treated and classified. For the performance analysis and comparison, a discrete-time statistical calculus is developed and applied to chaotic signal processing schemes. Discrete-time baseband models are developed, which are suitable for a statistical performance analysis. Analysis results for various example systems are provided and compared. New decoder structures are proposed and included in the comparative studies.