gebhart/patrepeval huggingface dataset:
PseudoCyc, A Pathway-Genome Database for <i>Pseudomonas aeruginosa</i> (2003)

A pathway-genome database (PGDB) describes the entire genome of an organism, as well as its biochemical pathways, reactions, and enzymes. Our PathoLogic software can generate a PGDB from an annotated genome of an organism, predicting the metabolic reactions and pathways corresponding to the enzymes present in the annotation. We have used PathoLogic to generate a PGDB for PSEUDOMONAS AERUGINOSA, strain PAO1, called 'PseudoCyc', which includes 139 predicted pathways and 800 predicted reactions involving 623 chemical species and 718 enzymes. Analysis of the PathoLogic predictions of arginine metabolism and the beta-ketoadipate pathway, which are landmark pathways in P. AERUGINOSA, showed that they were for the most part correctly predicted. These studies also provided possible locations for two genes involved in the beta-ketoadipate pathway, PCAI and PCAJ, which are missing from the PAO1 annotation. PseudoCyc adds an extended dimension to the genome of P. AERUGINOSA, providing researchers with a helpful tool for the analysis of the genomic, proteomic, and metabolic information of the organism. The finding of the probable location of the PCAI and PCAJ genes is but one example of the discoveries facilitated by such a PGDB. PseudoCyc, along with PGDBs for 12 other organisms, is available at http://BioCyc.org/.
Occupational Dermatitis from Soldering Flux (2004)

The aim of this study was to determine the specific agent responsible for eczema on the forearms of 2 electronic assemblers who cleaned out a flux-spraying unit once a week. Soldering flux can be a source of skin irritation as well as allergy. Patch test with dried flux residue (as is) and rosin in dilution series of 20%, 10%, and 1% in olive oil was performed. Readings were taken on day 2 and day 3. The rosin in dilution series was negative; however, the flux residue gave a + reaction on day 2, and by day 3 the reaction had weakened (+?). Similar results were obtained in 2 unexposed controls. Patch tests results in our cases indicate that the flux used in the soldering process caused irritant contact dermatitis.
Pharmacological control of human basophil histamine release stimulated by eosinophil granule major basic protein. (1989)

Eosinophil granule major basic protein (MBP) is a 13,800 MW arginine-rich polypeptide that is unique among basic molecules in its ability to stimulate human basophil histamine release. We examined the Ca2+ requirements and pharmacological regulation of MBP-stimulated histamine release. Minimal MBP-induced histamine release occurred in the absence of extracellular Ca2+, whereas addition of 0.1 mM Ca2+ resulted in 70% of the maximum histamine release response. Maximum histamine release required 0.5 to 1 mM extracellular Ca2+. The MBP-induced histamine release was blocked by a calmodulin antagonist and by theophylline and was partially inhibited by an inhibitor of phospholipase A2. Release was unaffected by inhibition of protein kinase C. Basophil pretreatment with pertussis toxin also resulted in a concentration-dependent inhibition of release, suggesting involvement of a GTP regulatory protein in the activation mechanism. Histamine release stimulated by a 13,900 MW poly-L-arginine exhibited a dissimilar pharmacological profile from that of MBP. These results support the non-cytolytic nature of the MBP activation mechanism and identify pharmacological approaches for control of MBP-induced mediator release.
Strained-Germanium Nanostructures for Infrared Photonics (2014)

The controlled application of strain in crystalline semiconductors can be used to modify their basic physical properties to enhance performance in electronic and photonic device applications. In germanium, tensile strain can even be used to change the nature of the fundamental energy band gap from indirect to direct, thereby dramatically increasing the interband radiative efficiency and allowing population inversion and optical gain. For biaxial tension, the required strain levels (around 2%) are physically accessible but necessitate the use of very thin crystals. A particularly promising materials platform in this respect is provided by Ge nanomembranes, that is, single-crystal sheets with nanoscale thicknesses that are either completely released from or partially suspended over their native substrates. Using this approach, Ge tensilely strained beyond the expected threshold for direct-band gap behavior has recently been demonstrated, together with strong strain-enhanced photoluminescence and evidence of population inversion. We review the basic properties, state of the art, and prospects of tensilely strained Ge for infrared photonic applications.
In Situ Growth of Self-assembled Indium Islands in Close Proximity to Semiconductor Quantum Emitters (2014)

Self-assembled indium islands on III-V quantum dot (QD) samples with a 7nm cap show a 4x enhancement in the peak intensity of the PL offering a bottom-up platform for studying the resonant coupling between plasmonic structures and semiconductor quantum emitters.
Body Ascendant: Modernism and the Physical Imperative (review) (2002)

The illustrations to Harold B. Segel's Body Ascendant: Modernism and the Physical Imperative chart a peculiar path through the first half of the twentieth century. From theatrical pantomimes and German expressionist dance, through physical education movements, bodybuilding, and naked gymnastics, the illustrations culminate in a photograph from a Hitler Youth track meet. However reductionist, the trajectory of these illustrations approximates Segel's deterministic account of the body's place in the art, and then the politics of the first half of the twentieth century. According to Segel, "the Holocaust, in its way, can be understood as the last stage, the extreme fulfillment, of the modernist obsession with physicality" (8). [End Page 176]
THE IDENTIFICATION AND EVALUATION OF COLLEGE EFFECTS ON STUDENT ACHIEVEMENT1 (1969)

ABSTRACT A sample of 6855 students from 95 colleges was used in an attempt to identify groups of colleges with students showing high achievement relative to initial aptitude. College means on the Scholastic Aptitude Test obtained at college entrance were used as a control measure for differences in initial aptitude. Student achievement was measured by college means on the Graduate Record Examination Area Tests obtained from the same students as upperclassmen. Measures of college characteristics were used to form subgroups of colleges. Although the correlations between the aptitude means and the achievement means were quite high, certain college characteristics, particularly college income per student and the proportion of faculty with a doctorate, did distinguish high achieving groups of colleges from low achieving groups.
Standards and Impact of Hematopathology in Myelodysplastic Syndromes (MDS) (2010)

The diagnosis, classification, and prognostication of patients with myelodysplastic syndromes (MDS) are usually based on clinical parameters, analysis of peripheral blood and bone marrow smears, and cytogenetic determinants. However, a thorough histologic and immunohistochemical examination of the bone marrow is often required for a final diagnosis and exact classification in these patients. Notably, histology and immunohistology may reveal dysplasia in megakaryocytes or other bone marrow lineages and/or the presence of clusters of CD34-positive precursor cells. In other cases, histology may reveal an unrelated or co-existing hematopoietic neoplasm, or may support the conclusion the patient is suffering from acute myeloid leukemia rather than MDS. Moreover, histologic investigations and immunohistology may reveal an increase in tryptase-positive cells, a coexisting systemic mastocytosis, or bone marrow fibrosis, which is of prognostic significance. To discuss diagnostic algorithms, terminologies, parameters, and specific issues in the hematopathologic evaluation of MDS, a Working Conference involving a consortium of US and EU experts, was organized in June 2010. The outcomes of the conference and resulting recommendations provided by the faculty, are reported in this article. These guidelines should assist in the diagnosis, classification, and prognostication in MDS in daily practice as well as in clinical trials.
ChemInform Abstract: SYNTHESIS OF DIASTEREOMERIC INDOLE DERIVATIVES FROM AZOMETHINES AND HOMOPHTHALIC ANHYDRIDES. ONE‐STEP PREPARATION OF HEXADEHYDROYOHIMBANS (1978)

Abstract Das Homophthalsäureanhydrid (Ia) reagiert mit den Indolylazomethinen (II) zu den isomeren Carbonsäuren (i)‐(IIIa) und (i)‐(IVa), die als Methylester (i)‐(IIIb) und (i)‐(IVb) charakterisiert werden.
Multimode fibres for micro-endoscopy (2015)

Abstract There has been a tremendous effort in modern microscopy towards miniaturisation and fibre-based technology, driven by the need to access hostile or difficult environments in situ and in vivo. Most of these rely on reducing the size of endoscopes based on fibre-optic bundles, and systems incorporating microfabricated lenses. Recently, the use of standard multimode optical fibres for lensless microscopy has become possible mainly due to advances in holographic beam shaping. This article reviews the methods and techniques behind this progress paving theway towards minimally invasive in vivo imaging as well as other applications of multimode waveguides including on-chip integration of optical micro-manipulation and numerous other biophotonics techniques.
SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site (2017)

The DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA-binding domains using a refined version of SELEX-seq. We developed an algorithm, <i>SelexGLM</i>, that quantifies binding specificity over a large (31-bp) binding site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15-bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly(A) sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers.
Provence romaine : Pellerin (Pierre), Le chanoine Sautel exhume Vaison-la-Romaine, La Colombe (Éditions du Vieux-Colombier), Paris, 1954 (1955)

Labrousse Michel. Provence romaine : Pellerin (Pierre), Le chanoine Sautel exhume Vaison-la-Romaine, La Colombe (Editions du Vieux-Colombier), Paris, 1954. In: Annales du Midi : revue archeologique, historique et philologique de la France meridionale, Tome 67, N°29, 1955. pp. 68-69.
Degradation of Human Antimicrobial Peptide LL-37 by <i>Staphylococcus aureus</i> -Derived Proteinases (2004)

Cathelicidin LL-37 is one of the few human bactericidal peptides with potent antistaphylococcal activity. In this study we examined the susceptibility of LL-37 to proteolytic degradation by two major proteinases produced by Staphylococcus aureus, a metalloproteinase (aureolysin) and a glutamylendopeptidase (V8 protease). We found that aureolysin cleaved and inactivated LL-37 in a time- and concentration-dependent manner. Analysis of the generated fragments by mass spectroscopy revealed that the initial cleavage of LL-37 by aureolysin occurred between the Arg19-Ile20, Arg23-Ile24, and Leu31-Val32 peptide bonds, instantly annihilating the antibacterial activity of LL-37. In contrast, the V8 proteinase hydrolyzed efficiently only the Glu16-Phe17 peptide bond, rendering the C-terminal fragment refractory to further degradation. This fragment (termed LL-17-37) displayed antibacterial activity against S. aureus at a molar level similar to that of the full-length LL-37 peptide, indicating that the antibacterial activity of LL-37 resides in the C-terminal region. In keeping with LL-37 degradation by aureolysin, S. aureus strains that produce significant amounts of this metalloprotease were found to be less susceptible to LL-17-37 than strains expressing no aureolysin activity. Taken together, these data suggest that aureolysin production by S. aureus contributes to the resistance of this pathogen to the innate immune system of humans mediated by LL-37.
A Reappraisal of Reliability and Validity Studies in Stroke (1996)

The identification of the most reliable stroke classifications and scales should encourage their use in selection of homogeneous populations of patients for clinical research studies and to improve communication among scientists. Further research is needed to investigate neglected aspects of the neurological examination and the validity of stroke classifications.
Author Response (1991)

We agree with Dr Binder-Macleod that therapists should not change their clinical practice on the basis of our study. This is because the purpose of the investigation was not to define the optimal conditions for activating quadriceps femoris muscles (as Binder-Macleod mistakenly stated in his commentary), but to investigate factors that influenced the magnitude of electrically induced torque. In that study, despite the possibility that we might not have administered neuromuscular electrical stimulation (NMES) under conditions that were optimal for NMES-induced torque (as stated in points 1 and 2 of the commentary), it is highly unlikely that the relative contributions that were measured would be in error. Is there a reason to believe that physiological factors that affect submaximal torque would be different than those that affect maximal torque? We disagree with the point that no systematic investigation of electrode size was undertaken.
A retrospective look at Greenstone (2007)

The Greenstone Digital Library Software has helped spread the practical impact of digital library technology throughout the world, with particular emphasis on developing countries. As Greenstone enters its second decade, this article takes a retrospective look at its development, the challenges that have been faced, and the lessons that have been learned in developing and deploying a comprehensive open-source system for the construction of digital libraries internationally. Not surprisingly, the most difficult challenges have been political, educational, and sociological, echoing that old programmers' blessing "may all your problems be technical ones.".
Ultrasonic technique for the investigation of structural properties of biological fluids (1999)

Biological fluids are specific objects for acoustical investigation due to the wide spectra of relaxation processes, especially nonstationary fluids such as blood during its coagulation process. The proposed method combines measurement of ultrasound attenuation over a frequency range and, ultrasound velocity dispersion being negligible, precise measurement of velocity variations at fixed frequency. In the dynamic spectroscopy method the wideband ultrasonic signal transmitted through the media is digitized with a sample rate of 200 MHz, averaged, and processed by a PC. Ultrasound absorption frequency dependency with intervals of 1 min is determined from amplitude spectra. Using small volume (1 ml) cell with multiple reflections, in the range of 2–17-MHz, diffraction corrections and ultrasonic attenuation were determined in low-absorptive standard liquid, conservative, and native coagulating blood. The clot formation process in the native blood is also monitored at frequencies 5 or 10 MHz using the time-of-flight method with the acquisition of the results. In the cell of 0.2 ml volume sensitivity of 0.2 ns is achieved. Cell parameters and influence of the pulse bandwidth are analyzed. According to the ultrasound velocity variations, four typical blood coagulation phases were observed during 30 min, less expressed being the first phase (0–2 min).
[CT-guided hookwire localization of small solitary pulmonary nodules in video-assisted thoracoscopic surgery]. (2009)

The preoperative CT-guided hookwire localization for small solitary pulmonary nodules is an effective and safe technique to assist VATS resection of the nodules.
Brain TRH receptors are the same as pituitary TRH receptors (1983)

Journal Article Brain TRH receptors are the same as pituitary TRH receptors Get access P W Dettmar, P W Dettmar Department of Pharmacology, Reckitt and Colman, Pharmaceutical Division, Dansom Lane, Hull HU8 7DS, U.K. Correspondence. Department of Pharmacology, Reckitt and Colman, Pharmaceutical Division, Dansom Lane, Hull HU8 7DS, U.K. Search for other works by this author on: Oxford Academic Google Scholar A G Lynn, A G Lynn Department of Pharmacology, Reckitt and Colman, Pharmaceutical Division, Dansom Lane, Hull HU8 7DS, U.K. Search for other works by this author on: Oxford Academic Google Scholar G Metcalf, G Metcalf Department of Pharmacology, Reckitt and Colman, Pharmaceutical Division, Dansom Lane, Hull HU8 7DS, U.K. Search for other works by this author on: Oxford Academic Google Scholar B A Morgan B A Morgan Department of Pharmacology, Reckitt and Colman, Pharmaceutical Division, Dansom Lane, Hull HU8 7DS, U.K. Search for other works by this author on: Oxford Academic Google Scholar Journal of Pharmacy and Pharmacology, Volume 35, Issue 6, June 1983, Pages 399–400, https://doi.org/10.1111/j.2042-7158.1983.tb02970.x Published: 12 April 2011 Article history Received: 18 November 1982 Published: 12 April 2011
Recursive calculation of the two-dimensional maximum likelihood position estimate for a scintillation camera (1990)

Maximum likelihood position estimation of a scintillation event in a gamma-ray imaging detector has been described using two independent one-dimensional estimates in x and y. This approximation is only valid when the sampled light-spread function is separable, and spatial distortion is observed when this constraint is violated. Recursive calculation of the 2-D position estimate using a sequence of one-dimensional estimates was investigated. Mean phototube response functions were computed from Monte Carlo simulations of the light-spread function, and position was estimated for scintillation events using recursive estimation. After three steps the maximum errors were mod delta x mod =0.04 mm and mod delta y mod =0.06 mm for the case of noise-free data and when mean response functions were known at each estimated location. Using response functions interpolated over 6-mm intervals gave increased distortion with average x and y errors of 0.097 and 0.082 mm, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Spontaneous CD8 T Cell Responses against the Melanocyte Differentiation Antigen RAB38/NY-MEL-1 in Melanoma Patients (2006)

The melanocyte differentiation Ag RAB38/NY-MEL-1 was identified by serological expression cloning (SEREX) and is expressed in the vast majority of melanoma lesions. The immunogenicity of RAB38/NY-MEL-1 has been corroborated previously by the frequent occurrence of specific Ab responses in melanoma patients. To elucidate potential CD8 T cell responses, we applied in vitro sensitization with overlapping peptides spanning the RAB38/NY-MEL-1 protein sequence and the reverse immunology approach. The identified peptide RAB38/NY-MEL-1(50-58) exhibited a marked response in ELISPOT assays after in vitro sensitization of CD8 T cells from HLA-A *0201(+) melanoma patients. In vitro digestion assays using purified proteasomes provided evidence of natural processing of RAB38/NY-MEL-1(50-58) peptide. Accordingly, monoclonal RAB38/NY-MEL-1(50-58)-specific T cell populations were capable of specifically recognizing HLA-A2(+) melanoma cell lines expressing RAB38/NY-MEL-1. Applying fluorescent HLA-A2/RAB38/NY-MEL-1(50-58) multimeric constructs, we were able to document a spontaneously developed memory/effector CD8 T cell response against this peptide in a melanoma patient. To elucidate the Ag-processing pathway, we demonstrate that RAB38/NY-MEL-1(50-58) is produced efficiently by the standard proteasome and the immunoproteasome. In addition to the identification of a RAB38/NY-MEL-1-derived immunogenic CD8 T cell epitope, this study is instrumental for both the onset and monitoring of future RAB38/NY-MEL-1-based vaccination trials.
Certain Characteristics of Formation of Conditioned Reflexes in Sheep. (1928)

The defensive reaction evoked by the application of an electric shock to the sheep's foreleg is a convenient unconditioned reflex from which to develop various conditioned reflexes. Six lambs born in May, 1928, were, after about 18 days preliminary training in August, caused to develop auditory conditioned reflexes of the simultaneous type. That is, the auditory stimulus signalling an electric shock preceded the shock by a short, variable interval of 2 to 6 seconds. The conditioned stimulus for 2 of the lambs was the sound of a buzzer. For the others it was the sound of the metronome beating twice per second. The conditioned reflex appeared in the 6 animals after 3 to 7 combinations of sound and shock and became relatively stable (11 or more positive conditioned responses in succession) after 18 to 43 combinations. The development of a conditioned reflex of the type described and a simple maze habit exhibit a common characteristic. Both show a period of instability between the first appearance of the new response and the final, more or less stereotyped, reaction. The most interesting feature of the formation of the conditioned reflex was the concentration of the motor response with increasing training. At first, the reaction involved a widespread activity of the skeletal musculature. The leg receiving the shock might be extended instead of flexed as the animal struggled in the harness. Later, and usually before the conditioned reflex was stable, the response was gradually concentrated in the leg stimulated by the electric current and the sound now evoked a brief and precise leg movement. The reaction of the other skeletal muscles at this stage served to give the body a posture in which the foreleg could be vigorously flexed.