gebhart/patrepeval huggingface dataset:
Comparison of fine‐needle aspiration cytology and core biopsy for diagnosis of breast cancer (2001)

Both fine-needle aspiration (FNA) cytology and core biopsy are useful in the diagnosis of breast cancer. In order to compare the sensitivities of these procedures, we reviewed 209 patients with breast cancer who had either FNA, core biopsy, or both, and also either mastectomy or lumpectomy. Sensitivities for FNA and core biopsies for diagnosing breast cancer were calculated and compared. Sensitivity for FNA or core biopsies interpreted as either atypical or malignant was 93.8% for FNA and 90.1% for core biopsy (P > 0.05). Sensitivity for FNA or core biopsies interpreted as malignant was 65.4% for FNA and 88.7% for core biopsy (P < 0.0001). Sensitivities of FNA interpreted as either atypical or malignant were 92.4% for FNA performed by pathologists and 100% for FNA by nonpathologists (P > 0.05). Sensitivities of FNA interpreted as malignant were 75.8% for FNA by pathologists and 20.0% for FNA by nonpathologists (P < 0.00001). Both FNA and core biopsies are sensitive procedures for the detection of breast cancer. There was no significant difference between sensitivity of FNA and core biopsies interpreted as either atypia or malignancy, although the sensitivity of core biopsies interpreted as unequivocal malignancy was greater than that of FNA. FNAs performed by pathologists were more sensitive than FNAs performed by nonpathologists in making an unequivocal diagnosis of breast cancer.
Reactive Power and Voltage Control in Distribution Systems With Limited Switching Operations (2009)

An algorithm based on a nonlinear interior-point method and discretization penalties is proposed in this paper for the solution of the mixed-integer nonlinear programming (MINLP) problem associated with reactive power and voltage control in distribution systems to minimize daily energy losses, with time-related constraints being considered. Some of these constraints represent limits on the number of switching operations of transformer load tap changers (LTCs) and capacitors, which are modeled as discrete control variables. The discrete variables are treated here as continuous variables during the solution process, thus transforming the MINLP problem into an NLP problem that can be more efficiently solved exploiting its highly sparse matrix structure; a strategy is developed to round these variables off to their nearest discrete values, so that daily switching operation limits are properly met. The proposed method is compared with respect to other well-known MINLP solution methods, namely, a genetic algorithm and the popular GAMS MINLP solvers BARON and DICOPT. The effectiveness of the proposed method is demonstrated in the well-known PG&E 69-bus distribution network and a real distribution system in the city of Guangzhou, China, where the proposed technique has been in operation since 2003.
A 5-year-old white girl with Prader-Willi syndrome and a submicroscopic deletion of chromosome 15q11q13 (1996)

We report on a 5-year-old white girl with Prader-Willi syndrome (PWS) and a submicroscopic deletion of 15q11q13 of approximately 100-200 kb in size. High resolution chromosome analysis was normal but fluorescence in situ hybridization (FISH), Southern hybridization, and microsatellite data from the 15q11q13 region demonstrated that the deletion was paternal in origin and included the SNRPN, PAR-5, and PAR-7 genes from the proximal to distal boundaries of the deletion segment. SNRPN and PW71B methylation studies showed an abnormal pattern consistent with the diagnosis of PWS and supported the presence of a paternal deletion of 15q11q13 or an imprinting mutation. Biparental (normal) inheritance of PW71B (D15S63 locus) and a deletion of the SNRPN gene were observed by microsatellite, quantitative Southern hybridization, and/or FISH analyses. Our patient met the diagnostic criteria for PWS, but has no reported behavior problems, hyperphagia, or hypopigmentation. Our patient further supports SNRPN and possibly other genomic sequences which are deleted as the cause of the phenotype recognized in PWS patients.
TMPRSS2 Contributes to Virus Spread and Immunopathology in the Airways of Murine Models after Coronavirus Infection (2019)

Transmembrane serine protease TMPRSS2 activates the spike protein of highly pathogenic human coronaviruses such as severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV). <i>In vitro</i>, activation induces virus-cell membrane fusion at the cell surface. However, the roles of TMPRSS2 during coronavirus infection <i>in vivo</i> are unclear. Here, we used animal models of SARS-CoV and MERS-CoV infection to investigate the role of TMPRSS2. Th1-prone C57BL/6 mice and TMPRSS2-knockout (KO) mice were used for SARS-CoV infection, and transgenic mice expressing the human MERS-CoV receptor DPP4 (hDPP4-Tg mice) and TMPRSS2-KO hDPP4-Tg mice were used for MERS-CoV infection. After experimental infection, TMPRSS2-deficient mouse strains showed reduced body weight loss and viral kinetics in the lungs. Lack of TMPRSS2 affected the primary sites of infection and virus spread within the airway, accompanied by less severe immunopathology. However, TMPRSS2-KO mice showed weakened inflammatory chemokine and/or cytokine responses to intranasal stimulation with poly(I·C), a Toll-like receptor 3 agonist. In conclusion, TMPRSS2 plays a crucial role in viral spread within the airway of murine models infected by SARS-CoV and MERS-CoV and in the resulting immunopathology.<b>IMPORTANCE</b> Broad-spectrum antiviral drugs against highly pathogenic coronaviruses and other emerging viruses are desirable to enable a rapid response to pandemic threats. Transmembrane protease serine type 2 (TMPRSS2), a protease belonging to the type II transmembrane serine protease family, cleaves the coronavirus spike protein, making it a potential therapeutic target for coronavirus infections. Here, we examined the role of TMPRSS2 using animal models of SARS-CoV and MERS-CoV infection. The results suggest that lack of TMPRSS2 in the airways reduces the severity of lung pathology after infection by SARS-CoV and MERS-CoV. Taken together, the results will facilitate development of novel targets for coronavirus therapy.
Use of the δ-P_1 approximation for recovery of optical absorption, scattering, and asymmetry coefficients in turbid media (2004)

We introduce a robust method to recover optical absorption, reduced scattering, and single-scattering asymmetry coefficients (microa, micro's, g1) of infinite turbid media over a range of (micro's/microa) spanning 3 orders of magnitude. This is accomplished through the spatially resolved measurement of irradiance at source-detector separations spanning 0.25-8 transport mean free paths (l*). These measurements are rapidly processed by a multistaged nonlinear optimization algorithm in which the measured irradiances are compared with predictions given by the delta-P1 variant of the diffusion approximation to the Boltzmann transport equation. The ability of the delta-P1 model to accurately describe radiative transport within media of arbitrary albedo and on spatial scales comparable to l* is the key element enabling the separation of g1 from micro's.
Geographic Information Science: Defining the Field (2003)

In the last decade, Geographic Information Science has emerged as a focus of considerable academic attention. To some extent, it is the Earth’s New Science, just as Cognitive Science was the Mind’s New Science a decade or two earlier (Gardner, 1985). But it is not clear how deep or lasting the impact of GI Science will be, either on academia or on the GIS industry. Rather than following the success of Cognitive Science, GI Science could just as easily be the next Regional Science, a similar fusion of disciplines that peaked early and continues today mainly as an internally successful multidisciplinary field of relatively low influence on science, technology, or society. Worse yet, Geographic Information Science could largely be just a pretentious name for Geographic Information Systems, and not really a scientific or intellectual field at all. This paper seeks to explore these issues, and to lay out the intellectual scope of Geographic Information Science.
Sialic Acid-Containing Milk Proteins Show Differential Immunomodulatory Activities Independent of Sialic Acid (2005)

The immunomodulatory activities of four sialic acid-containing milk proteins (kappa-casein, glycomacropeptide, lactoferrin, and proteose peptone-3 component) were determined, and the role of sialic acid was evaluated. Two in vitro models were used: murine splenocyte proliferation, where the effect on LPS-, Con A-, and PHA-stimulated proliferation was studied, and cytokine production in LPS-stimulated murine dendritic cells (DC). All four proteins inhibited LPS-induced splenocyte proliferation, though to different degrees, and independently of sialic acid. kappa-Casein strongly inhibited PHA-induced proliferation and had a weak inhibitory effect on Con A-induced proliferation, whereas lactoferrin stimulated Con A-induced proliferation. kappa-Casein, glycomacropeptide, and lactoferrin differentially affected cytokine production by DC: kappa-casein significantly inhibited production of TNF-alpha, IL-10, -12, -6, and -1beta, independent of sialic acid, whereas less-marked effects of glycomacropeptide and lactoferrin were seen. These findings thus point to important immunosuppressive effects of some milk proteins and indicate that they may function via different mechanisms.
Theory of Electron Band Tails and the Urbach Optical-Absorption Edge (1986)

The density of states $\ensuremath{\rho}(E)$ in the tail for an electron in a correlated Gaussian random potential in three dimensions is constructed from first principles by means of a simple physical argument. This yields a linear exponential dependence of $\ensuremath{\rho}$ on $E$ which, for reasonable values of the rms potential fluctuation and correlation length, spans many decades, and occupies most of the experimentally observable energy range. This is suggested as the origin of the fundamental Urbach optical-absorption edge.
A Defective Pentose Phosphate Pathway Reduces Inflammatory Macrophage Responses during Hypercholesterolemia (2018)

Metabolic reprogramming has emerged as a crucial regulator of immune cell activation, but how systemic metabolism influences immune cell metabolism and function remains to be investigated. To investigate the effect of dyslipidemia on immune cell metabolism, we performed in-depth transcriptional, metabolic, and functional characterization of macrophages isolated from hypercholesterolemic mice. Systemic metabolic changes in such mice alter cellular macrophage metabolism and attenuate inflammatory macrophage responses. In addition to diminished maximal mitochondrial respiration, hypercholesterolemia reduces the LPS-mediated induction of the pentose phosphate pathway (PPP) and the Nrf2-mediated oxidative stress response. Our observation that suppression of the PPP diminishes LPS-induced cytokine secretion supports the notion that this pathway contributes to inflammatory macrophage responses. Overall, this study reveals that systemic and cellular metabolism are strongly interconnected, together dictating macrophage phenotype and function.
Design and code inspections to reduce errors in program development (1976)

We can summarize the discussion of design and code inspections and process control in developing programs as follows: 1. Describe the program development process in terms of operations, and define exit criteria which must be satisfied for completion of each operation. 2. Separate the objectives of the inspection process operations to keep the inspection team focused on one objective at a time: Operation Overview Preparation Inspection Rework Follow-up Objective Communications/education Education Find errors Fix errors Ensure all fixes are applied correctly 3. Classify errors by type, and rank frequency of occurrence of types. Identify which types to spend most time looking for in the inspection. 4. Describe how to look for presence of error types. 5. Analyze inspection results and use for constant process improvement (until process averages are reached and then use for process control).
Novel alignment technique for surface stabilized ferroelectric liquid crystal (1990)

An alignment method for obtaining excellent surface stabilized ferroelectric liquid-crystal devices is described. Alignment is obtained by obliquely depositing the SiO in two steps. The first deposition involves vacuum coating at 60° angle and the second at 85° (orthogonally to the first) with the substrate normal. The method induces a high (∼20°–25°) pretilt surface which depends on the thickness of the second layer. The glass substrates are matched with antiparallel direction of evaporation of second coating. This ensures a selective pretilt of molecules and the uniformly tilted smectic layer structure. The advantages of this new method are the ease of large-scale production, defect-free large uniform monodomains, good contrast, bistability, and microsecond switching speed response.
The Expression of P-Glycoprotein and Cellular Kinases Is Modulated at the Transcriptional Level by Infection and Highly Active Antiretroviral Therapy in a Primate Model of AIDS (2003)

The beneficial effects of highly active antiretroviral therapy (HAART) in HIV-infected patients may be limited by inadequate compliance and viral resistance, but also by host cell factors, such as P-glycoprotein (P-gp) and intracellular kinases involved in the phosphorylation of nucleoside reverse transcriptase inhibitors. We investigated the effects of infection and HAART (zidovudine [AZT], lamivudine [3TC], and indinavir [IDV] on the expression of P-gp and cell kinases involved in the phosphorylation of AZT and 3TC in SHIV89.6P-infected cynomolgus macaques. Under unstimulated conditions, we observed a decrease in P-gp mRNA levels in the peripheral blood and lymph node mononuclear cells of infected macaques, which was accentuated by HAART. SHIV infection also resulted in the overexpression of thymidine kinase mRNA, which was abolished by HAART. In conclusion, retroviral infection and HAART modulate in vivo at the transcriptional level the expression of host cell factors that may affect the efficacy of HAART.
First cryogenic electro-optic switch on silicon with high bandwidth and low power tunability (2018)

We demonstrate the first electro-optic switch operating at cryogenic temperatures of 4 K with a high electrooptic bandwidth of > 18 GHz. Our novel technology exploits the Pockels effect in barium titanate thin films co-integrated with silicon photonics and offers low losses, pure phase modulation, and sub-pW electro-optic tuning.
Selective Arylsulfonamide Inhibitors of ADAM-17: Hit Optimization and Activity in Ovarian Cancer Cell Models (2013)

Activated leukocyte cell adhesion molecule (ALCAM) is expressed at the surface of epithelial ovarian cancer (EOC) cells and is released in a soluble form (sALCAM) by ADAM-17-mediated shedding. This process is relevant to EOC cell motility and invasiveness, which is reduced by inhibitors of ADAM-17. In addition, ADAM-17 plays a key role in EGFR signaling and thus may represent a useful target in anticancer therapy. Herein we report our hit optimization effort to identify potent and selective ADAM-17 inhibitors, starting with previously identified inhibitor 1. A new series of secondary sulfonamido-based hydroxamates was designed and synthesized. The biological activity of the newly synthesized compounds was tested in vitro on isolated enzymes and human EOC cell lines. The optimization process led to compound 21, which showed an IC50 of 1.9 nM on ADAM-17 with greatly increased selectivity. This compound maintained good inhibitory properties on sALCAM shedding in several in vitro assays.
Cleavage and Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein by Human Airway Trypsin-Like Protease (2011)

The highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) poses a constant threat to human health. The viral spike protein (SARS-S) mediates host cell entry and is a potential target for antiviral intervention. Activation of SARS-S by host cell proteases is essential for SARS-CoV infectivity but remains incompletely understood. Here, we analyzed the role of the type II transmembrane serine proteases (TTSPs) human airway trypsin-like protease (HAT) and transmembrane protease, serine 2 (TMPRSS2), in SARS-S activation. We found that HAT activates SARS-S in the context of surrogate systems and authentic SARS-CoV infection and is coexpressed with the viral receptor angiotensin-converting enzyme 2 (ACE2) in bronchial epithelial cells and pneumocytes. HAT cleaved SARS-S at R667, as determined by mutagenesis and mass spectrometry, and activated SARS-S for cell-cell fusion in cis and trans, while the related pulmonary protease TMPRSS2 cleaved SARS-S at multiple sites and activated SARS-S only in trans. However, TMPRSS2 but not HAT expression rendered SARS-S-driven virus-cell fusion independent of cathepsin activity, indicating that HAT and TMPRSS2 activate SARS-S differentially. Collectively, our results show that HAT cleaves and activates SARS-S and might support viral spread in patients.
Aortic endothelial cell migration. I. Matrix requirements and composition. (1982)

Endothelial cell migration was studied following a mechanical injury produced in cultured confluent monolayers of calf aortic endothelium with the use of a quantitative migration assay. In this method the cells were grown on glass coverslips coated with scarlet red-containing Formvar. At confluency, the cultures were cut in half with a blade; one half was removed with the pigmented Formvar, and the other was returned to culture. Migration was linear for a least 96 hours, and was due to cell motility, not proliferation. Since it was blocked in the presence of L-azetidine carboxylic acid or cis-hydroxyproline, inhibitors of collagen secretion, endothelial cell migration appeared to be dependent on the continual secretion of collagen. Furthermore, the types, apparent relative amounts, and localizations of the collagens as well as laminin changed during the migratory process. These studies support the notion that the aortic endothelial cell migratory response to injury is a dynamic one requiring the continual secretion and modulation of matrix molecules.
Periodontal healing of canine experimental grade-III furcation defects treated with autologous fibrinogen and absorbable barrier membrane (1998)

Use of AF and ABM did not enhance the amount of periodontal healing, compared with debridement only. The ABM-treated defects were essentially devoid of root ankylosis. Grade-III furcation defects may respond equally well to conservative periodontal surgery or guided tissue regenerative techniques. The prevention of root ankylosis is a substantial benefit favoring this latter method of treatment.
Image Denoising by Pointwise Thresholding of the Undecimated Wavelet Coefficients: A Global Sure Optimum (2007)

We devise a new undecimated wavelet thresholding for denoising images corrupted by additive Gaussian white noise. The first key point of our approach is the use of a linearly parameterized pointwise thresholding function. The second key point consists in optimizing the parameters globally by minimizing Stein's unbiased MSE estimate (SURE) directly in the image-domain, and not separately in the wavelet subbands. Amazingly, our method gives similar results to the best state-of-the-art algorithms, despite using only a simple pointwise thresholding function; we demonstrate it in simulations over a wide range of noise levels for a representative set of standard grayscale images.
Antithymocyte globulin treatment of severe aplastic anaemia (1983)

Nineteen patients with severe aplastic anaemia were treated with antithymocyte globulin. Ten patients obtained remissions (transfusion independent, at least 45000 platelets and 2000 PMN/mm3) within 2-3 months and continue in remission 5-35 months after antithymocyte globulin. Ages of responders ranged from 17 to 71. Complications of antithymocyte globulin included arthralgias, rash, serum sickness, angioedema and fever. Two patients died during, two shortly after, and one 10 months after therapy. One patient with a previous remission following antithymocyte globulin relapsed and achieved a second remission with retreatment. Previous androgen therapy did not affect outcome since two of four patients with and eight of 15 patients without previous androgen therapy achieved remission with ATG. Treatment with antithymocyte globulin is a promising alternative to bone marrow transplantation in the treatment of severe aplastic anaemia.
Alkene Pulsed Plasma Functionalized Surfaces: An Interfacial Diels‐Alder Reaction Study (2005)

This chapter contains sections titled: Abstract Introduction Materials and Methods Results and Discussion Interfacial Chemistry Cycloaddition Kinetics Monolayers Plasma Polymer Thin Films Comparison of Surface Reaction in Monolayers and Plasma Polymer Thin Films Conclusion References
Ultrathin Film Electrodeposition of Polythiophene Conjugated Networks through a Polymer Precursor Route (2001)

The electrodeposition of polysiloxane precursor polymers to form cross-linked conjugated polythiophene ultrathin films is described. The precursor polymer contains a polysiloxane backbone with pendant electroactive thiophene monomer units synthesized via a hydrosilylation reaction. The thiophene units were electropolymerized by cyclic voltammetry. Investigations were made on the oxidation and reduction of the thiophene monomer and the polymers formed. A uniformly smooth layer-by-layer growth of the film was observed by repeated cycling based on the cyclic voltammogram, surface plasmon spectroscopy (SPS), and the atomic force microscopy images. The morphology of the film changed with increasing number of cycles being transformed from a relatively globular to a more membranelike morphology. Correlation was also made on the morphological changes with the electropolymerization process and the extent of cross-linking. UV−vis spectra showed clear evidence of polythiophene structure formation in the cross-linked polymer. SPS confirmed that the thickness of the deposited polymer film is easily controlled by the number of electrochemical potential cycles.
Wissenschaft, Alltag und System: Ein Thema und seine Variationen (1988)

Die Differenz zwischen weitgespannten theoretischen Modellen und empirischen Detailstudien, die sich nur mühsam oder auch gar nicht aufeinander beziehen lassen, ist sicher kein Merkmal nur der Sozialwissenschaften; die im Kuhnschen Sinne normale Wissenschaft der Naturwissenschaften hat in ihrer Alltäglichkeit, wie bekannt, mit großer Theorie nur wenig und mit dem Zusammentragen mühsamer und häufig irrelevanter Einzelergebnisse äußerst viel zu tun. Der institutionalisierte Wissenschaftsbetrieb scheint eine derartige Differenz auch fast zu erzwingen: Die notwendige spezialisierende Arbeitsteilung, die sowohl eine zwischen Themenbereichen als auch eine zwischen theoretischer und empirischer Arbeit ist, führt mit einer gewissen Zwangsläufigkeit dazu, daß theoretische und empirische Erfassung von Themenbereichen entweder unverbunden nebeneinander herlaufen oder daß quasi modische Anleihen bei den jeweilig anderen Spezialisten gemacht werden — die dann freilich ohne wirksame Folgen bleiben.