gebhart/patrepeval huggingface dataset:
Two ‘<i>Candidatus</i> Liberibacter asiaticus’ Strains Recently Found in California Harbor Different Prophages (2017)

'Candidatus Liberibacter asiaticus' (CLas), an α-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, two cases of CLas have been detected in Los Angeles County, one in Hacienda Heights in 2012 and the other in San Gabriel in 2015. Although all infected trees were destroyed in compliance with a state mandate, citrus industry stakeholder concerns about HLB in California are high. Little is known about the biology of CLas, particularly the California strains, hindering effective HLB management efforts. In this study, next-generation sequencing technology (Illumina MiSeq) was employed to characterize the California CLas strains. Data sets containing >4 billion (Giga) bp of sequence were generated from each CLas sample. Two prophages (P-HHCA1-2 and P-SGCA5-1) were identified by the MiSeq read mapping technique referenced to two known Florida CLas prophage sequences, SC1 and SC2. P-HHCA1-2 was an SC2-like or Type 2 prophage of 38,989 bp in size. P-SGCA5-1 was an SC1-like or Type 1 prophage of 37,487 bp in size. Phylogenetic analysis revealed that P-HHCA1-2 was part of an Asiatic lineage within the Type 2 prophage group. Similarly, P-SGCA5-1 was part of an Asiatic lineage within Type 1 prophage group. The Asiatic relatedness of both P-HHCA1-2 and P-SGCA5-1 was further presented by single nucleotide polymorphism analysis at terL (encoding prophage terminase) that has been established for CLas strain differentiation. The presence of different prophages suggests that the two California CLas strains could have been introduced from different sources. An alternative explanation is that there was a mixed CLas population containing the two types of prophages, and limited sampling in a geographic region may not accurately depict the true CLas diversity. More accurate pathway analysis may be achieved by including more strains collected from the regions.
Recognizing creative needs in user interface design (2002)

The creative process requires experimentation, the exploration of variations, and the continual evaluation of one's progress. While these processes are frequently non-linear and iterative, modern user interfaces do not explicitly support these practices, and instead impose a linear progression through tasks that is a poor fit for creative pursuits. In this paper we use data from three case studies, and draw upon Sch$#246;n's theory of reflection-in-action to illustrate specific deficiencies in current user interfaces when used in creative endeavors. We then develop a set of guidelines for user interface design and demonstrate their application in three designs intended to support tasks in the domain of image manipulation.
Fractions Derived from Soy Beans and Navy Beans Which Retard Tryptic Digestion of Casein (1944)

Aqueous extracts of soy beans or navy beans contain a fraction which inhibits the in vitro digestion of milk casein by trypsin. The fraction can be precipitated with acetone. It is partially heat labile at pH 4. Its presence may account for the low nutritive value of raw soy and navy beans.
Prolonged allograft survival in anti-CD4 antibody transgenic mice: lack of residual helper T cells compared with other CD4-deficient mice. (2000)

The GK5 mice, with a complete absence of peripheral CD4 cells, provide the cleanest available model for investigating the role of CD4 lymphocytes in allograft rejection. Prolonged skin allograft survival in these mice compared with CD4 and MHC class II KO recipients was clearly the result of improved CD4 depletion. Nevertheless, skin allograft rejection, heart allograft infiltration, and vascular disease, mediated by CD8 cells, developed in the absence of peripheral CD4 T cells.
Correlated and uncorrelated timing jitter in gain-switched laser diodes (1993)

The author describes correlated and uncorrelated timing jitter of gain-switched pulses generated from sinusoidally modulated laser diodes measured from photocurrent power spectra. It is found that if dc bias is decreased to obtain shorter pulses, then the root-mean-square (rms) value of uncorrelated timing jitter drastically increases to more than 2 ps, while correlated jitter remains constant at the drive circuit level of approximately 0.2 ps. By optimizing the bias condition and compression fiber length, total timing jitter of gain-switched pulses can be reduced to as low as approximately 0.5 ps, as their pulse width is kept less than 10 ps.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Emerging drugs for alpha-1-antitrypsin deficiency (2010)

A1AT deficiency is a good model to investigate the role of inflammation and proteolytic enzymes in the pathophysiology of COPD. Augmentation therapy is expensive but restores the deficiency to normal and current evidence suggests this ameliorates progression of the disease. Understanding the mechanisms involved has led to the development of newer strategies to protect the lung and liver from the development of disease but efficacy and safety concerns require careful introduction of these strategies. Although the condition is relatively common in the Northern hemisphere, the ability to deliver conventional Phase III clinical trials with lung physiology as the primary outcome will be limited by the sensitivity of the tests and number of patients required.
Differential signalling and glutamate receptor compositions in the OFF bipolar cell types in the mouse retina (2015)

The retina is the entrance to the visual system, which receives various kinds of image signals and forms multiple encoding pathways. The second-order retinal neurons, the bipolar cells, are thought to initiate multiple neural streams by encoding various visual signals in different types of cells. However, the functions of each bipolar cell type have not been fully understood. We investigated whether OFF bipolar cells encode visual signals in a type-dependent manner. We recorded the changes in the bipolar cell voltage in response to two input functions: step and sinusoidal light stimuli. Type 1 and 4 OFF bipolar cells were sustained cells and responded to sinusoidal stimuli over a broad range of frequencies. Type 2 and 3a cells were transient and exhibited band-pass filtering. Type 3b cells were in the middle of these two groups. The distinct temporal responses might be attributed to different types of glutamate receptors. We examined the AMPA and kainate glutamate receptor composition in each bipolar cell type. The light responses in the transient OFF bipolar cells were exclusively mediated by kainate receptors. Although the kainate receptors mediated the light responses in the sustained cells, the AMPA receptors also mediated a portion of the responses in sustained cells. Furthermore, we found that some types of cells were rectified more than other types. Taken together, we found that the OFF bipolar cells encode diverse temporal image signals in a type-dependent manner, confirming that each type of OFF bipolar cell initiates diverse temporal visual processing in parallel.
ChemInform Abstract: Oxometalates Containing Boron Islands, Ni5MB2O10. (1989)

Abstract Single crystals of the hitherto unknown title compounds with M: Ge or Zr are obtained from melts of the components NiO:MO2 = 5:1 in the presence of B 2 O 3 as a flux at 1300‐1400 °C. The isotypic compounds crystallize in the space group Pbam with Z=2.
Co<sup>II</sup>/Zn<sup>II</sup>–(<scp>L</scp>‐Tyrosine) Magnetic Metal–Organic Frameworks (2012)

Abstract Three chiral coordination polymers assembled from L ‐tyrosine ( L ‐tyr) and cobalt, cobalt/zinc and zinc salts, with a new three‐dimensional (3D) structure and formulated as [M( L ‐tyr)] n (M = Co, Co/Zn, Zn) have been prepared by mild hydrothermal synthesis. These three compounds are isostructural, crystallize with monoclinic symmetry in the C 2 space group and possess four crystallographically unique metal sites in tetrahedral (two) and octahedral (two) coordination environments resulting in two slightly distinct edge‐sharing metal dimers with L ‐tyr linking the metal atoms in pillars. These features result in a dense framework. The study of the magnetic properties of the cobalt‐bearing solid reveals a ferromagnetic exchange interaction within the Co 2+ dimers. The racemic compound of dl ‐tyrosine and cobalt was also synthesized and its structure characterized.
Quality work improvement groups (1994)

Continuous quality improvement has resulted in the need for the development of new and exciting skills in group dynamics and in the facilitation of small group interactions. Leaders of quality work groups must use the understanding of group dynamics and leadership to maintain high performance work teams. To be effective, the team leaders and members must be aware of what is being said (content) and how things are being said (processes). Team leaders and groups can not be guaranteed effectiveness. However, development of the necessary skills in team building will ensure the likelihood of effective group processes and positive outcomes.
3-D heart contour delineation and motion tracking of ultrasound images using continuous distance transform neural networks (2002)

We apply the previously proposed continuous distance transform neural network (CDTNN) to effectively represent the 3-D endocardial (inner) and epicardial (outer) contours and track the motion of the left ventricle (principal pumping chamber) of the heart from ultrasound images. This CDTNN has many good properties as the conventional distance transforms which are suitable for 3-D object representation and deformation estimation. In addition, this continuous and differentiable representation is parametric so that very low memory storage is needed. We have successfully represented the 3-D epicardial and endocardial walls of the left ventricle of the heart using CDTNNs based on 7.5% to 25% of manually traced training data. The absolute error measured compares favorably with the human interobserver variability reported for analyzing distances.
Towards commercial products by nanocasting: characterization and lithium insertion properties of carbons with a macroporous, interconnected pore structure (2012)

Carbon materials with defined porosity are prepared using the nanocasting approach. The structural properties of the prepared carbon materials are examined by SEM, XRD, XPS, elemental analysis, nitrogen physisorption and Hg porosimetry. The materials exhibit an interconnected porous network with spherical pores in the macropore range, being a replica of spherical SiO2 particles. The average macropore size (300–700 nm) and surface area (35–470 m2 g−1) can be tailored by the choice of template and carbon precursor. More importantly, based on silica templates prepared by flame pyrolysis, the whole process, including HF etching of the template, can be easily industrialized. Lithium storage measurements are used to demonstrate the beneficial transport properties of the porous carbon materials which are referenced against non-porous carbons. The porous carbon materials exhibit high capacity (550 mA h g−1 at C/5) and excellent rate capability (90 mA h g−1 at 60C). Surprisingly, the excellent lithium storage properties are related to the macroporous framework rather than high surface area and/or micro- and mesoporosity.
An Injectable Hydrogel Prepared Using a PEG/Vitamin E Copolymer Facilitating Aqueous-Driven Gelation (2016)

Hydrogels have been widely explored for biomedical applications, with injectable hydrogels being of particular interest for their ability to precisely deliver drugs and cells to targets. Although these hydrogels have demonstrated satisfactory properties in many cases, challenges still remain for commercialization. In this paper, we describe a simple injectable hydrogel based on poly(ethylene glycol) (PEG) and a vitamin E (Ve) methacrylate copolymer prepared via simple free radical polymerization and delivered in a solution of low molecular weight PEG and Ve as the solvent instead of water. The hydrogel formed immediately in an aqueous environment with a controllable gelation time. The driving force for gelation is attributed to the self-assembly of hydrophobic Ve residues upon exposure to water to form a physically cross-linked polymer network via polymer chain rearrangement and subsequent phase separation, a spontaneous process with water uptake. The hydrogels can be customized to give the desired water content, mechanical strength, and drug release kinetics simply by formulating the PEGMA-co-Ve polymer with an appropriate solvent mixture or by varying the molecular weight of the polymer. The hydrogels exhibited no significant cytotoxicity in vitro using fibroblasts and good tissue compatibility in the eye and when injected subcutaneously. These polymers thus have the potential to be used in a variety of applications where injection of a drug or cell containing depot would be desirable.
Reaction of neopentane with hydrogen over Pd, Pt, Ir and Rh (1987)

The skeletal reaction of neopentane with dihydrogen has been studied over powders and (111) oriented films of palladium, platinum, iridium and rhodium. Various pretreatments of the metals have been used for changing the surface morphology (O2–H2 pretreatment, very high temperature reduction etc). The effect of O2–H2 pretreatment on the course of the reaction was most pronounced in case of palladium (selectivity change) and platinum (overall activity change). The catalytic behaviour of rhodium and iridium suffers only minor changes after these pretreatments: demethylation always predominates. In contrast to unsintered palladium, heavily annealed Pd samples should have a lower density of surface imperfections. This fact seems to be responsible for the negligible activity of sintered Pd surfaces in hydrogenolysis and, in effect, for the higher selectivity toward isomerization. XRD analysis of variously pretreated metal powders shows that the increase in isomerization selectivity may be attributed to the sintering of palladium. At ca. 200 °C iridium powder was only slightly selective toward isomerization (2–3 %). This selectivity is limited to the initial stage of the reaction only and to clean, but not carbided, surfaces of iridium. A carbided Ir surface produces unusually large amounts of ethane among the hydrogenolysis products. The comparison between catalytic behaviour of platinum and other Group VIII metals allows us to rationalize the results in terms of surface morphology and the reaction mechanism.
Adult-to-adult living related liver transplantation: initial experience. (2001)

The number of adult patients on the liver transplantation waiting lists is growing steadily. Adult living related liver transplantation (LRLT) represents the ultimate means to expand the donor pool. The success of this model of "small for size" grafting relies on strict donor and recipient selection. The choice of the graft (2 left and 4 right hepatectomies) was made on the minimal ratio between estimated graft and recipient body weights (0.8-1%), necessary to meet the recipient's metabolic demands. Our experience with six adults is reported. Donor morbidity was minimal (one wound infection); there was no mortality. Four (66%) recipients are doing well, two died of infectious complications. All recipients had a complicated post-transplant course. Due to its complexity, both in donor and recipient, LRLT should only be developed very carefully in experienced liver transplant centers.
Monomer-Monomer Interactions Drive the Prepore to Pore Conversion of a β-Barrel-forming Cholesterol-dependent Cytolysin (2002)

Perfringolysin O (PFO), a cholesterol-dependent cytolysin, forms large oligomeric pore complexes comprised of up to 50 PFO molecules. In the present studies a mutant of PFO (PFO(Y181A)) has been identified that traps PFO in a multimeric prepore complex that cannot insert its transmembrane beta-hairpins and therefore cannot form a pore. Remarkably, PFO(Y181A) can be induced to insert its transmembrane beta-hairpins if functional PFO is incorporated into the PFO(Y181A) oligomeric prepore complex. Furthermore, the transition from prepore to pore appears to be an "all or none" process; partial insertion of the transmembrane beta-barrel does not occur. Therefore, cooperative interactions between the monomers of the prepore drive the prepore to pore conversion that results in the formation of the transmembrane beta-barrel.
Mapping and Sequencing of RNAs without Recourse to Molecular Cloning: Application to RNAs of the Sabin 1 Strain of Poliovirus and Its Defective Interfering Particles1 (1986)

Complementary DNA to the genome of the Sabin 1 strain of poliovirus was prepared by reverse transcription with oligo(dT)10 as a primer and separated into six classes of DNA by their size. Each class of the DNA, after digestion with restriction endonuclease HaeIII, was analyzed by two-dimensional polyacrylamide gel electrophoresis. Comparison of the patterns of the restriction fragments led us to compose a possible arrangement of the restriction fragments on the viral genome. Sequence analysis of these fragments indicated that the arrangement was consistent with the known total nucleotide sequence of the genome. In the determined sequences, two bases were observed to differ from those of a cloned complementary DNA of the Sabin 1 genome. This suggested that the sequence of the cloned DNA reflected that of a mutated virus genome that was a minor component in the virus inoculation stock. The genomes of defective interfering particles generated from the Sabin 1 strain were also analyzed by this technique. The results suggested that the RNAs lacked an internal region of the Sabin 1 RNA encoding viral capsid proteins. The location of the deletion was further confirmed by determination of the nucleotide sequence of a cloned complementary DNA copy of the defective interfering particle RNA. Thus, the method described here is useful for mapping and sequencing of RNAs and for knowing whether cloned cDNAs represent the major population of RNA molecules or not.
Phytochelatin Synthesis and Glutathione Levels in Response to Heavy Metals in Tomato Cells (1987)

Cell suspension cultures of tomato, Lycopersicon esculentum Mill. cv VFNT-Cherry, produce phytochelatins (poly[gamma-glutamylcysteinyl]glycines) when exposed to cadmium. The synthesis of these peptides is accompanied by a decline in cellular levels of glutathione. Buthionine sulfoximine, an inhibitor of glutathione synthesis, inhibits the sustained production of phytochelatins. However, phytochelatin synthesis can occur in the presence of buthionine sulfoximine provided that sufficient glutathione is available. These results indicate that glutathione is a substrate for phytochelatin synthesis. The protein synthesis inhibitor cycloheximide does not affect the initial production of phytochelatin.
A Direct, Copper-Catalyzed Functionalization of Pyridines with Alkynes (2010)

A one-pot, copper-catalyzed method to construct 2-alk­ynylpyridines is presented. This provides a route to access these products directly from terminal alkynes and the parent pyridine, and without prefunctionalization of the pyridine core. In addition, (Z)-alk-2-enylpyridines can be prepared via a related procedure. These reactions are used to synthesize a number of new alkynyl- and alkenyl­-substituted pyridines in one pot.
[Indications for antidepressive agents in relation to diseases of the cardiovascular system]. (1993)

Antidepressants, in particular tricyclic ones (TCA), and inhibitors of monoaminooxidase (IMAO) exert a number of undesirable cardiovascular effects. TCA and IMAO frequently cause postural hypotension (PH). IMAO administration is associated with the risk of hypertensive crisis. TCA raises the heart rate and can cause abnormalities in the conduction of the cardiac excitation. TCA are contraindicated after myocardial infarction and are the cause of death after overdosage. When PH is undesirable, in hypertension and cardiac insufficiency the following safe antidepressants are recommended: nortriptyline, mianserine, trazodone and viloxazine. In abnormalities of conduction of the cardiac excitation and after myocardial infarction only mianserine, trazodione and viloxazine are recommended. With regard to cardiovascular toxicity, antidepressants from the series of selective inhibitors of serotonin reabsorption are very promising: fluvoxamine, fluoxetine, citalopram, paroxetine and sertraline. The same applies also to the reversible IMAO type A moclobemide.
Motuporamines, Anti-Invasion and Anti-Angiogenic Alkaloids from the Marine Sponge <i>Xestospongia </i><i>e</i><i>xigua </i>(Kirkpatrick):  Isolation, Structure Elucidation, Analogue Synthesis, and Conformational Analysis (2001)

Extracts of the sponge Xestospongia exigua collected in Papua New Guinea were positive in a new assay for anti-invasion activity. Bioassay-guided fractionation led to the identification of the three known motuporamines A (1), B (2), and C (3) along with the new motuporamines D (4), E (5), and F (6) and a mixture of G, H, and I (15). Motuporamines A (1), B (2), and C (3) and the mixture of G, H, and I (15) were responsible for the anti-invasion activity of the crude extract. Motuporamine C (3) has also been found to be anti-angiogenic. A series of analogues of the motuporamines have been synthesized and evaluated for anti-invasive activity. These SAR results revealed that a saturated 15-membered cyclic amine fused to the natural motuporamine diamine side chain (13) represented the optimal structure for anti-invasive activity in this family. Single-crystal X-ray diffraction analysis of one of the analogues 20 showed that in the solid state its 16-membered macrocyclic amine fragment adopted the [4444] quadrangular conformation predicted by calculations to be the lowest energy conformation for the corresponding cycloalkane, cyclohexadecane. These data along with literature X-ray data and conformational analysis for derivatives of azacyclotridecane have been used as precedents for predicting the lowest energy ring conformations of other motuporamines. The SAR data from the natural and synthetic motuporamines have been combined with the conformational analyses to provide an outline of the functionality and shape required for activity in this family of alkaloids and to design a new analogue 49 that showed good anti-invasion activity.
Synthesis of Optically Active .ALPHA.-Phenylpyridylmethanols with Baker's Yeast. (1994)

We have synthesized optically active alpha-phenylpyridylmethanols by using free baker's yeast (FBY) in water, immobilized baker's yeast (IMBY) in water, and IMBY in hexane.