gebhart/patrepeval huggingface dataset:
Reconciling Trust and Modularity Goals in Web Services (2009)

Web services are distributed software components, that are decoupled from each other using interfaces with specified functional behaviors. However, such behavioral specifications are insufficient to demonstrate compliance with certain temporal non-functional policies. We show an example demonstrating that a patient's health-related query sent to a health care service is answered only by a doctor (and not by a secretary). Demonstrating compliance with such policies is important for satisfying governmental privacy regulations. It is often necessary to expose the internals of the web service implementation for demonstrating such compliance, which may compromise modularity. In this work, we provide a language design that enables such demonstrations, while hiding majority of the service's source code. The key idea is to use greybox specifications to allow service providers to selectively hide and expose parts of their implementation. The overall problem of showing compliance is then reduced to two subproblems: whether the desired properties are satisfied by the service's greybox specification, and whether this greybox specification is satisfied by the service's implementation. We specify policies using LTL and solve the first problem by model checking. We solve the second problem by refinement techniques.
Impact of Conditioning Regimen Intensity on Outcome of Allogeneic Hematopoietic Cell Transplantation for Advanced Acute Myelogenous Leukemia and Myelodysplastic Syndrome (2006)

We reviewed 136 patients with advanced acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS) undergoing allogeneic transplantation to assess the impact of conditioning regimen intensity on outcome. Thirty-nine patients receiving nonmyeloablative stem cell transplantation (NST) were compared with 97 patients receiving myeloablative transplantation. Patients receiving NST were at high risk for treatment-related complications given that they were older, 57 vs 43 years (P < .001), and more likely had received previous or myeloablative transplantation (54% vs 2%; P < .0001). The cumulative risk of relapse was higher for patients after NST (61% vs 38%; P = .02). The 100-day mortality was less after NST (15% vs 32%) Overall survival (OS) at 2 years was 28% for NST and 34% for myeloablative transplantation (P = .89). Progression-free survival (PFS) at 2 years was 20% for NST and 31% for myeloablative transplantation (P = .31). Cox regression analysis showed that the intensity of the conditioning regimen had no effect on either OS or PFS. Despite the high-risk features of patients with advanced AML or MDS undergoing NST, OS and PFS in these patients was similar to those in patients receiving myeloablative transplantation. These results demonstrate that dose intensity plays a significant role in control of disease after transplantation, but that this benefit is negated by increasing treatment-related mortality. These results suggest that NST is a reasonable alternative for patients with advanced AML and MDS at high risk for complications after myeloablative transplantation.
DESIGN OF ROCK CHUTES (1998)

Rock chute design information is consolidated from several sources to provide a comprehensive design tool.The rock slope stability, boundary roughness, and outlet stability of rock chutes are each discussed. Tests were performedin three rectangular flumes and in two full size structures. Angular riprap with a median stone size ranging from 15 to278 mm was examined on rock chutes with slopes ranging from 2 to 40%. The typical mode of channel failure isdescribed. An empirical prediction equation is presented relating the highest stable discharge on a rock chute to themedian stone size and the bed slope. A boundary roughness relationship is also presented that relates the Manningroughness coefficient to the median stone size and bed slope. These tests also suggest that the riprap size required forstability on the slope will remain stable in the outlet reach even with minimal tailwater. This article contains informationneeded to perform a rock chute design.
Microsomal prostaglandin E synthase-1 (mPGES-1) is the primary form of PGES expressed by the primate periovulatory follicle (2005)

These data indicate that mPGES-1 is a gonadotropin-regulated PG synthesis enzyme expressed by granulosa cells of primate periovulatory follicles and suggest that mPGES-1 may be the primary PGES responsible for the increased follicular PGE2 levels necessary for primate ovulation.
PROFESSIONS AND BUSINESSES Medical Licenses: Provide for Teaching Licenses and for Review of Physician's Fitness to Practice Medicine (1987)

The Act allows the Composite State Board of Medical Examiners to grant, in its discretion, teaching licenses without an examination to doctors licensed in another state or foreign country. The Act also requires the Board to investigate a doctor's fitness to practice medicine when an insurer reports, pursuant to section 33-3-27, any medical malpractice judgment or settlement in excess of $100,000, or any two judgments or settlements. Finally, the Act requires doctors to report directly to the Board any settlements relating to the practice of medicine in excess of $20,000. July 1, 1987
Carbonyl iron for short‐term supplementation in female blood donors (1987)

A randomized, double-blind trial of iron replacement after repeated blood donation was conducted in 75 menstruating women; 51 completed the study. Volunteers were assigned randomly to one of three treatment groups: 1) carbonyl iron (nontoxic elemental iron powder), 600 mg; 2) ferrous sulfate, 300 mg (60 mg Fe++); or 3) placebo, each given three times daily for 1 week immediately after blood donation. Blood samples obtained initially and 56 days later were tested for hemoglobin, mean corpuscular volume (MCV), free erythrocyte protoporphyrin, serum ferritin, serum iron, total iron binding capacity (TIBC), and percent saturation of TIBC. The prevalence of gastrointestinal side effects was similar in both groups taking iron. At the end of the study there was no laboratory evidence of change in iron status in women who received carbonyl iron (n = 15). In those treated with ferrous sulfate (n = 17) the mean TIBC increased (p less than 0.001), and in the placebo group (n = 19) there were decreases in mean MCV (p less than 0.01), serum ferritin (p less than 0.001), and percent saturation (p = 0.027) with an increase in mean TIBC (p = 0.004). Carbonyl iron seems to be effective for short-term iron replacement in repeat blood donors and may have the advantage of decreased or absent risk of poisoning if accidentally ingested by children.
Importance of renal biopsy* (2001)

SUMMARY: Renal biopsy remains an essential requirement for the accurate diagnosis and treatment of several forms of renal disease. Recent advances in technique have improved the safety of the procedure. However, its use in certain categories of patients remains controversial. These include patients with diabetes or chronic renal failure and patients over the age of 60 years. This brief review addresses some of the advances in the biopsy procedure and its application to diseases of the native kidney.
Reaktionen CH‐aktiver Verbindungen mit Aziden, XXIII Synthese von α‐Diazo‐phosphonsäureestern (1968)

Abstract Die α‐Diazo‐phosphonsäureester 2a — g entstehen bei der Diazogruppen‐Übertragung mit p ‐Toluolsulfonsäureazid auf die PO‐aktivierten Methylenverbindungen 1a — g ; die analoge Umsetzung des Carbamoylmethanphosphonsäure‐diäthylesters ( 3 ) verläuft über das Diazo derivat 4 zum Triazol 5 . Die entformylierende Diazogruppen‐Übertragung versagt allerdings bei der Anwendung auf 2‐Oxo‐1‐phenyl‐äthanphosphonsäure‐diäthylester ( 6 ). Statt des erwarteten 2a wurde lediglich 4(5)‐Phenyl‐1.2.3‐triazol ( 9 ) erhalten; sein Entstehen wird über das Triazolin 8 gedeutet, das den Phosphono‐Rest in einer intramolekularen PO‐aktivierten Olefinierung abspaltet. Für die Synthese von hat sich vor allem die Bamford‐Stevens ‐Reaktion bewährt, die von 11 ausgehend über die syn‐anti ‐Isomeren 13 bzw. 12 , verläuft. Diäthylphosphono‐phenyl‐diazomethan ( 2a ) und das 4‐Nitro‐Derivat 2b addieren sich an Methyl‐vinyl‐keton zu den Δ 2 ‐Pyrazolinen 14a und b .
Mutations in 2 distinct genetic pathways result in cerebral cavernous malformations in mice (2011)

Cerebral cavernous malformations (CCMs) are a common type of vascular malformation in the brain that are a major cause of hemorrhagic stroke. This condition has been independently linked to 3 separate genes: Krev1 interaction trapped (KRIT1), Cerebral cavernous malformation 2 (CCM2), and Programmed cell death 10 (PDCD10). Despite the commonality in disease pathology caused by mutations in these 3 genes, we found that the loss of Pdcd10 results in significantly different developmental, cell biological, and signaling phenotypes from those seen in the absence of Ccm2 and Krit1. PDCD10 bound to germinal center kinase III (GCKIII) family members, a subset of serine-threonine kinases, and facilitated lumen formation by endothelial cells both in vivo and in vitro. These findings suggest that CCM may be a common tissue manifestation of distinct mechanistic pathways. Nevertheless, loss of heterozygosity (LOH) for either Pdcd10 or Ccm2 resulted in CCMs in mice. The murine phenotype induced by loss of either protein reproduced all of the key clinical features observed in human patients with CCM, as determined by direct comparison with genotype-specific human surgical specimens. These results suggest that CCM may be more effectively treated by directing therapies based on the underlying genetic mutation rather than treating the condition as a single clinical entity.
Three-Dimensional Microstructured Poly(vinyl alcohol) Hydrogel Platform for the Controlled Formation of Multicellular Cell Spheroids (2017)

Three-dimensional (3D) multicellular cell spheroids (MCSs) are excellent in vitro cell models, in which, e.g., the in vivo cell-cell interaction processes are much better mimicked than in conventional two-dimensional (2D) cell layers. However, the difficulties in the generation of well-defined MCSs with controlled size severely limit their application. Herein, low-adhesive poly(vinyl alcohol) (PVA) hydrogels structured with inverted pyramid-shaped microwells were used to guide the aggregation of cells into MCSs. The cells settling down into the microwells by gravity accumulated at the central tip of the wells and then gradually grew into spheroids. The size of cell spheroids can be straightforwardly controlled by the culture time and initially seeded cell number. The MCSs generated in a parallel microarray format were further used for drug testing. Our results suggest in agreement with complementary literature data that the cell culture format plays a critical role in the cellular response to drugs, and also confirms that spheroids possess a much higher drug resistance than cells in 2D layers. This novel microstructured PVA hydrogel is expected to offer a potential platform for the facile preparation of spheroids for various applications in the biomedical field.
Optically Polarized <sup>129</sup>Xe in NMR Spectroscopy* (1995)

Abstract 129 Xe has found widespread applications in NMR spectroscopy, but its use is often restricted by its low sensitivity and long relaxation times. Optical pumping of rubidium followed by spin exchange with xenon provides a well understood technique to enhance the 129 XePolarization by several orders of magnitude. The exploitation of this highly spin‐polarized xenon as a surface probe in NMR studies of various meterials is discussed. Applications of this technique make use not only of 129 Xe NMR detection, but also of the‐high spin polarization as a magnetization reservoir for selective cross‐polarization experiments to surface nuclei. A diverse variety of materials has been studied, ranging from mesoscopic structures such as semiconductor nanocrystals and porous silicon to high surface area polymers.
Oral Anticoagulant and Antiplatelet Therapy and Peripheral Arterial Disease (2007)

In patients with peripheral arterial disease, the combination of an oral anticoagulant and antiplatelet therapy was not more effective than antiplatelet therapy alone in preventing major cardiovascular complications and was associated with an increase in life-threatening bleeding. (ClinicalTrials.gov number, NCT00125671 [ClinicalTrials.gov].).
The NIMA-related kinase 2, Nek2, is expressed in specific stages of the meiotic cell cycle and associates with meiotic chromosomes (1997)

The Aspergillus nimA gene encodes a Ser/Thr protein kinase which is required for mitosis, in addition to Cdc2, and which has been suggested to have a role in chromosomal condensation. In this study, we isolated a potential murine homologue of nimA, Nek2, which was shown to be expressed most abundantly in the testis of the adult tissues examined. Its expression in the testis was restricted to the germ cells, with highest levels detected in spermatocytes at pachytene and diplotene stages. Immunohistochemical analysis revealed that Nek2 localized to nuclei, exhibiting a non-uniform distribution within the nucleus. Nek2 appeared to be associated with meiotic chromosomes, an association that was better defined by immunolocalization to hypotonically dispersed meiotic chromosomes. This localization was more apparent in regions of dense chromatin, including the sex vesicle, and was also obvious at some of the chromosome ends. The presence of Nek2 protein was not unique to male germ cells, as it was found in meiotic pachytene stage oocytes as well. Furthermore, in an in vitro experimental setting in which meiotic chromosome condensation was induced with okadaic acid, a concomitant induction of Nek2 kinase activity was observed. The expression of Nek2 in meiotic prophase is consistent with the hypothesis that in vivo, Nek2 is involved in the G2/M phase transition of the cell cycle. Our results further provide evidence that in vivo, mouse Nek2 is involved in events of meiosis, including but not limited to chromosomal condensation.
Human Mitogen-activated Protein Kinase CSBP1, but Not CSBP2, Complements a hog1 Deletion in Yeast (1995)

CSBP1 and CSBP2 are human homologues of the Saccharomyces cerevisiae Hog1 mitogen-activated protein kinase which is required for growth in high osmolarity media. Expression of CSBP1, but not CSBP2, complemented a hog1 delta phenotype. A CSBP2 mutant (A34V) that complements hog1 delta was isolated and found to have approximately 3-fold lower kinase activity than the wild-type CSBP2. Further analysis revealed that both the kinase activity and tyrosine phosphorylation of CSBP1 and CSBP2 (A34V) is regulated by salt. In contrast, wild-type CSBP2 is constitutively active but dependent on the upstream kinase, Pbs2. Mutagenesis studies showed that reduction or elimination of CSBP2 kinase activity restores salt responsiveness as measured by tyrosine phosphorylation suggesting that too high a level of kinase activity can result in desensitization of the host cell and inability to grow in high salt.
Interactive visual object search through mutual information maximization (2010)

Searching for small objects (e.g., logos) in images is a critical yet challenging problem. It becomes more difficult when target objects differ significantly from the query object due to changes in scale, viewpoint or style, not to mention partial occlusion or cluttered backgrounds. With the goal to retrieve and accurately locate the small object in the images, we formulate the object search as the problem of finding subimages with the largest mutual information toward the query object. Each image is characterized by a collection of local features. Instead of only using the query object for matching, we propose a discriminative matching using both positive and negative queries to obtain the mutual information score. The user can verify the retrieved subimages and improve the search results incrementally. Our experiments on a challenging logo database of 10,000 images highlight the effectiveness of this approach.
Gallium Disrupts Iron Metabolism of Mycobacteria Residing within Human Macrophages (2000)

Mycobacterium tuberculosis and M. avium complex (MAC) enter and multiply within monocytes and macrophages in phagosomes. In vitro growth studies using standard culture media indicate that siderophore-mediated iron (Fe) acquisition plays a critical role in the growth and metabolism of both M. tuberculosis and MAC. However, the applicability of such studies to conditions within the macrophage phagosome is unclear, due in part to the absence of experimental means to inhibit such a process. Based on the ability of gallium (Ga(3+)) to concentrate within mononuclear phagocytes and on evidence that Ga disrupts cellular Fe-dependent metabolic pathways by substituting for Fe(3+) and failing to undergo redox cycling, we hypothesized that Ga could disrupt Fe acquisition and Fe-dependent metabolic pathways of mycobacteria. We find that Ga(NO(3))(3) and Ga-transferrin produce an Fe-reversible concentration-dependent growth inhibition of M. tuberculosis strains and MAC grown extracellularly and within human macrophages. Ga is bactericidal for M. tuberculosis growing extracellularly and within macrophages. Finally, we provide evidence that exogenously added Fe is acquired by intraphagosomal M. tuberculosis and that Ga inhibits this Fe acquisition. Thus, Ga(NO(3))(3) disruption of mycobacterial Fe metabolism may serve as an experimental means to study the mechanism of Fe acquisition by intracellular mycobacteria and the role of Fe in intracellular survival. Furthermore, given the inability of biological systems to discriminate between Ga and Fe, this approach could have broad applicability to the study of Fe metabolism of other intracellular pathogens.
IMMOBILIZATION OF CELLULASE ON NON-POROUS ULTRAFINE SILICA PARTICLES (2007)

The immobilization of cellulase onto non-porous ultrafine silica particles was studied. Cellulase was extracted from a Trichoderma reesei culture after partial purification with ammonium sulfate (pH = 5.0), which was then immobilized onto non-porous ultrafine silica particles, with or without the use of glutaraldehyde as a crosslinking agent. Cellulase was immobilized by adsorption onto ultrafine silica particles efficiently, as well as by covalent cross-linking with glutaraldehysde. Increasing the concentration of the free form of enzyme increased the amount of immobilized cellulase. The maximum enzyme immobilization happened at the free enzyme concentration of 0.48 mg/ml. In general, the optimum pH for immobilization was found to be 5.0, which is close to the pI of the enzyme. The relative activity of the immobilized enzyme was also increased as the amount of immobilized enzyme was increased. However, immobilization of the enzyme on the ultrafine silica particles, with or without the use of glutaraldehyde, showed almost the same enzyme activities. The immobilized cellulase showed a higher thermal stability, with respect to temperature, compared to the free cellulase.
Bench-to-bedside review: The gut as an endocrine organ in the critically ill (2010)

In health, hormones secreted from the gastrointestinal tract have an important role in regulating gastrointestinal motility, glucose metabolism and immune function. Recent studies in the critically ill have established that the secretion of a number of these hormones is abnormal, which probably contributes to disordered gastrointestinal and metabolic function. Furthermore, manipulation of endogenous secretion, physiological replacement and supra-physiological treatment (pharmacological dosing) of these hormones are likely to be novel therapeutic targets in this group. Fasting ghrelin concentrations are reduced in the early phase of critical illness, and exogenous ghrelin is a potential therapy that could be used to accelerate gastric emptying and/or stimulate appetite. Motilin agonists, such as erythromycin, are effective gastrokinetic drugs in the critically ill. Cholecystokinin and peptide YY concentrations are elevated in both the fasting and postprandial states, and are likely to contribute to slow gastric emptying. Accordingly, there is a rationale for the therapeutic use of their antagonists. So-called incretin therapies (glucagon-like peptide-1 and glucose-dependent insulinotropic polypeptide) warrant evaluation in the management of hyperglycaemia in the critically ill. Exogenous glucagon-like peptide-2 (or its analogues) may be a potential therapy because of its intestinotropic properties.
A universal approximation of grain size from images of noncohesive sediment (2010)

The two‐dimensional spectral decomposition of an image of sediment provides a direct statistical estimate, grid‐by‐number style, of the mean of all intermediate axes of all single particles within the image. We develop and test this new method which, unlike existing techniques, requires neither image processing algorithms for detection and measurement of individual grains, nor calibration. The only information required of the operator is the spatial resolution of the image. The method is tested with images of bed sediment from nine different sedimentary environments (five beaches, three rivers, and one continental shelf), across the range 0.1 mm to 150 mm, taken in air and underwater. Each population was photographed using a different camera and lighting conditions. We term it a “universal approximation” because it has produced accurate estimates for all populations we have tested it with, without calibration. We use three approaches (theory, computational experiments, and physical experiments) to both understand and explore the sensitivities and limits of this new method. Based on 443 samples, the root‐mean‐squared (RMS) error between size estimates from the new method and known mean grain size (obtained from point counts on the image) was found to be ±≈16%, with a 95% probability of estimates within ±31% of the true mean grain size (measured in a linear scale). The RMS error reduces to ≈11%, with a 95% probability of estimates within ±20% of the true mean grain size if point counts from a few images are used to correct bias for a specific population of sediment images. It thus appears it is transferable between sedimentary populations with different grain size, but factors such as particle shape and packing may introduce bias which may need to be calibrated for. For the first time, an attempt has been made to mathematically relate the spatial distribution of pixel intensity within the image of sediment to the grain size.
The CXC Chemokines Gamma Interferon (IFN-γ)-Inducible Protein 10 and Monokine Induced by IFN-γ Are Released during Severe Melioidosis (2000)

Gamma interferon (IFN-gamma)-inducible protein 10 (IP-10) and monokine induced by IFN-gamma (Mig) are related CXC chemokines which bind to the CXCR3 receptor and specifically target activated T lymphocytes and natural killer (NK) cells. The production of IP-10 and Mig by various cell types in vitro is strongly dependent on IFN-gamma. To determine whether IP-10 and Mig are released during bacterial infection in humans, we measured plasma levels of IP-10 and Mig in patients with melioidosis, a severe gram-negative infection caused by Burkholderia pseudomallei. IP-10 and Mig were markedly elevated in patients with melioidosis on admission, particularly in blood culture-positive patients, and remained elevated during the 72-h study period. Levels of IP-10 and Mig showed a positive correlation with IFN-gamma concentrations and also correlated with clinical outcome. In whole blood stimulated with heat-killed B. pseudomallei, neutralization of IFN-gamma and tumor necrosis factor alpha (TNF-alpha) partly attenuated IP-10 and Mig release, while anti-interleukin-12 (IL-12) and anti-IL-18 had a synergistic effect. Stimulation with other bacteria or endotoxin also induced strong secretion of IP-10 and Mig. These data suggest that IP-10 and Mig are part of the innate immune response to bacterial infection. IP-10 and Mig may contribute to host defense in Th1-mediated host defense during infections by attracting CXCR3(+) Th1 cells to the site of inflammation.