gebhart/patrepeval huggingface dataset:
The Hierarchical Dependence Diagram: improving design for reuse in object-oriented software development (2002)

Object-oriented paradigm promises a high level of reusability in software development. However, by just selecting an object-oriented programming language does not guarantee achieving highly reusable software components. Reusable components have to be designed carefully from the early stage of software development. Among many proposed guidelines for improving software reusability, "class independence" is regarded as an important criterion. The guidelines in this category state that the less dependence the class is, the more reusable the class is. However we argue that the use of these guidelines is often very difficult to follow consistently within a group of designers during the design process. This is because the implementation of such guidelines is highly based on individual designer's interpretation and experience. Another problem is that such guidelines are difficult to apply to a large software system, which may consist of hundreds or even thousands of classes. This paper describes a new notation, called the Hierarchical Dependence Diagram (HDD), to support a more systematic use of "components independence" guidelines by extending reusable classes to "clusters", "libraries", and "platforms". Our work establishes a solid basis for tool support for improving reusability and can be more effectively applied to the development of large object-oriented software systems.
Coitus during Pregnancy (1985)

The effect of coitus on pregnancy outcome has been a subject of debate for more than 30 years. Previous studies, which purport to show an association between coitus and adverse outcome, have been based on inadequate data. The present authors have investigated the effect of coitus on outcome by means of prospectively collected data from 39,217 women in the Collaborative Perinatal Project. The proportion of women reporting coitus during the previous month declined with advancing gestation. Several factors were associated with coital frequency at different times of gestation. White women were more likely than black women to have coitus at all times up to 37 weeks, after which the reverse was true. Greater maternal and paternal age had significant and independent negative effects on coital frequency at all times of gestation. The cumulative life-table probability of delivery for women reporting different coital frequencies at 28–29 weeks is shown in Figure 1. There was no association between coitus and early delivery (P < 0.001). The same negative association was seen when women were stratified by coitus at 32 to 33 weeks. Women who had any historical or pregnancy-related complication were eliminated. Fig. 1. Cumulative probability of delivery by gestational age for women with different coital frequencies at 28–29 weeks. Overall probability of equality of the curves <0.001. This study in addition to revealing no relationship of coital frequency to premature delivery, or abortion, shows no increased perinatal mortality that could be correlated with coital frequency during pregnancy.
Modelización de flujos en el análisis input-output a partir de la teoría de redes (2010)

Las teorias de grafos y redes sociales han aportado una linea fructifera de investigacion 
en el analisis input-output a partir del estudio descriptivo de las relaciones productivas y las 
posiciones de los sectores en el entramado economico. 
Actualmente, nuevos estudios en el campo de las redes sociales se centran en las propias 
relaciones y en la explicacion de sus interdependencias y organizacion. El estudio de los factores 
que intervienen en el establecimiento de las relaciones es una tarea compleja que requiere el 
desarrollo de modelos estadisticos especificos. Dada la interdependencia sectorial existente en 
toda tabla input-output, estos modelos deben construirse lejos de los postulados de independencia 
de observaciones presente en la mayoria de las modelizaciones estadisticas. En este trabajo, bajo 
el enfoque de la teoria de redes, se propone el desarrollo de modelos, bajo el supuesto de 
dependencia estadistica, que permitan explicar la probabilidad de la estructura observada y 
evaluar la significatividad de diferentes efectos estructurales.
Genomic Potential of Stenotrophomonas maltophilia in Bioremediation with an Assessment of Its Multifaceted Role in Our Environment (2016)

The gram negative bacterium Stenotrophomonas is rapidly evolving as a nosocomial pathogen in immuno-compromised patients. Treatment of Stenotrophomonas maltophilia infections is problematic because of their increasing resistance to multiple antibiotics. This article aims to review the multi-disciplinary role of Stenotrophomonas in our environment with special focus on their metabolic and genetic potential in relation to bioremediation and phytoremediation. Current and emerging treatments and diagnosis for patients infected with S. maltophilia are discussed besides their capability of production of novel bioactive compounds. The plant growth promoting characteristics of this bacterium has been considered with special reference to secondary metabolite production. Nano-particle synthesis by Stenotrophomonas has also been reviewed in addition to their applications as effective biocontrol agents in plant and animal pathogenesis.
Long-Range Order in an Organic Overlayer Induced by Surface Reconstruction: Coronene on Ge(111) (2014)

Using scanning tunneling microscopy, we show that coronene molecules form supramolecular structures upon room-temperature deposition on Ge(111), in full commensurability with the c(2 × 8) reconstruction of the clean surface. The molecules are not adsorbed in a planar manner in the first layer; the balance between lateral intermolecular interactions and directional bonding to the surface forces them into a tilted configuration. Further coronene deposition leads to the formation of large domains of weakly bonded molecules adsorbed on top of the first layer. The ordering of the second layer is dictated by both, the first layer of molecules and the unaltered reconstructed substrate underneath. We provide a detailed analysis of the encountered molecular periodicities and discuss the mechanisms that lead to long-range ordering in these layers.
Molecular pathogenesis of rheumatic fever and rheumatic heart disease (2005)

Molecular mimicry between streptococcal and human proteins has been proposed as the triggering factor leading to autoimmunity in rheumatic fever (RF) and rheumatic heart disease (RHD). This article summarises studies on genetic susceptibility markers involved in the development of RF/RHD. It also focuses on the molecular mimicry in RHD mediated by the responses of B and T cells of peripheral blood, and T cells infiltrating heart lesions, against streptococcal antigens and human tissue proteins. The molecular basis of T-cell recognition is assessed through the definition of heart-crossreactive antigens. The production of cytokines from peripheral and heart-infiltrating mononuclear cells suggests that T helper 1 (Th1)-type cytokines are the mediators of RHD heart lesions. An insufficiency of interleukin 4 (IL-4)-producing cells in the valvular tissue might contribute to the maintenance and progression of valve lesions.
An Asymmetric Aldol−Ring-Closing Metathesis Strategy for the Enantioselective Construction of Oxygen Heterocycles:  An Efficient Approach to the Enantioselective Synthesis of (+)-Laurencin (1999)

A strategy is described for the enantioselective construction of medium-ring cyclic ethers by merging the asymmetric aldol addition of glycolates with a ring-closing metathesis reaction. Cyclic ethers of seven-, eight-, and nine-membered rings are readily available through a ring-closing metathesis without cyclic conformational constraints, by exploiting the acyclic conformational bias of the gauche effect. A short formal synthesis of the eight-membered ether (+)-laurencin, a red algae metabolite, has been accomplished utilizing the aldol−metathesis combination.
Risk factors for lactic acidosis and severe hyperlactataemia in HIV-1-infected adults exposed to antiretroviral therapy (2007)

Hyperlactataemia/lactic acidosis was associated with exposure to dideoxynucleosides, female gender, advanced immunosuppression and possibly ethnicity. This has important consequences for choice of ART in resource-limited settings. The association with shorter duration of exposure may support the hypothesis of susceptibility in a small proportion of patients.
p300 Acetyltransferase Regulates Androgen Receptor Degradation and PTEN-Deficient Prostate Tumorigenesis (2014)

Overexpression of the histone acetyltransferase p300 is implicated in the proliferation and progression of prostate cancer, but evidence of a causal role is lacking. In this study, we provide genetic evidence that this generic transcriptional coactivator functions as a positive modifier of prostate tumorigenesis. In a mouse model of PTEN deletion-induced prostate cancer, genetic ablation of p300 attenuated expression of the androgen receptor (AR). This finding was confirmed in human prostate cancer cells in which PTEN expression was abolished by RNA interference-mediated attenuation. These results were consistent with clinical evidence that the expression of p300 and AR correlates positively in human prostate cancer specimens. Mechanistically, PTEN inactivation increased AR phosphorylation at serine 81 (Ser81) to promote p300 binding and acetylation of AR, thereby precluding its polyubiquitination and degradation. In support of these findings, in PTEN-deficient prostate cancer in the mouse, we found that p300 was crucial for AR target gene expression. Taken together, our work identifies p300 as a molecular determinant of AR degradation and highlights p300 as a candidate target to manage prostate cancer, especially in cases marked by PTEN loss.
Towards a scalable search and query engine for the web (2007)

Current search engines do not fully leverage semantically rich datasets, or specialise in indexing just one domain-specific dataset.We present a search engine that uses the RDF data model to enable interactive query answering over richly structured and interlinked data collected from many disparate sources on the Web.
Thiacrown ether tetrathiafulvalene derivatives as redox responsive ligands (1999)

Thiacrown ether TTF derivatives have been synthesized; one of them, whose X-ray molecular structure has been determined, is shown to combine Ag+ recognition and reversible binding properties as a function of the electrochemical potential applied.
Effect of Whey Proteins, Their Oligopeptide Hydrolysates and Free Amino Acid Mixtures on Growth and Nitrogen Retention in Fed and Starved Rats (1989)

The effects of alimentary whey proteins given, as whole proteins (WP), controlled trypsin and chymotrypsin hydrolysate oligopeptides (WPH), or a free amino acid mixture (AAM), on growth, nitrogen retention, and steatorrhea were assessed in 24 Wistar rats (250 to 300 g) after 72 hr of starvation and 24 to 96 hr of realimentation and in 24 controls. The three diets had the same caloric, nitrogen, vitamin, and mineral contents. Rats had free access to the liquid diets. Only rats which ate the whole diet (90 cal) were included in the study. No differences in steatorrhea and fecal nitrogen were observed. The absorption rate was over 95% on the three diets. In contrast, weight gain was statistically better on WPH (+9% after 96 hr of realimentation) than on WP (+5%) or AAM (+2%). This was associated with a statistically higher nitrogen retention at all time periods studied, which was a result of a significant lower nitrogen urinary excretion. Similar results were obtained in controls. This better growth was a result of a better protein synthesis and lower ureagenesis.
The Effect of Doxazosin, Finasteride and Combination Therapy on Nocturia in Men With Benign Prostatic Hyperplasia (2007)

Doxazosin and combination therapy reduced nocturia more than placebo, but the net benefit of active drug compared to placebo was often modest with a net difference of less than 0.20 fewer nightly nocturia episodes at 1 and 4 years. Findings in men 70 years old or older were similar, with an even smaller effect observed for finasteride.
Naringenin Protects HaCaT Human Keratinocytes Against UVB‐induced Apoptosis and Enhances the Removal of Cyclobutane Pyrimidine Dimers from the Genome<sup>†</sup> (2007)

Many naturally occurring agents are believed to protect against UV-induced skin damage. In this study, we have investigated the effects of naringenin (NG), a naturally occurring citrus flavonone, on the removal of UVB-induced cyclobutane pyrimidine dimers (CPD) from the genome and apoptosis in immortalized p53-mutant human keratinocyte HaCaT cells. The colony-forming assay shows that treatment with NG significantly increases long-term cell survival after UVB irradiation. NG treatment also protects the cells from UVB-induced apoptosis, as indicated by the absence of the 180 base pair DNA ladders and the appearance of sub-G1 peak using agarose gel electrophoresis and flow cytometric analysis, respectively. The UVB-induced poly (ADP-ribose) polymerase-1 (PARP-1) cleavage, caspase activation and Bax/Bcl2 ratio were modulated following NG treatment, indicating an antiapoptotic effect of NG in UVB-damaged cells that occurs at least in part via caspase cascade pathway. Moreover, treatment of UVB-irradiated HaCaT cells with NG enhances the removal of CPD from the genome, as observed by both direct quantitation of CPD in genomic DNA and immuno-localization of the damage within the nuclei. The study provides a molecular basis for the action of NG as a promising natural flavonoid in preventing skin aging and carcinogenesis.
Dynamic Self-Assembly of Polymer Colloids To Form Linear Patterns (2005)

A dynamic self-assembling process is reported which involves drying a droplet of positively charged colloidal suspension on a flat negatively charged hydrophilic surface. This extremely simple method affords lines of colloidal particles with regular 1.5-4.5 microm line spacing and smaller than 2 microm line width over a broad surface area. The ordered region diffracts light to display an iridescent appearance and generates first-order diffraction spots when illuminated by a He-Ne laser. A periodic stick-slip motion of the drying liquid front is observed during the drying process using optical microscopy. The periodic motion must be related to the periodic particle deposition. We propose that the simultaneous deposition of the particles at a fixed distance (i.e., the line spacing) behind the previous line of particles where the contact line is pinned is in turn responsible for the periodic stick-slip motion. The key distinguishing feature of the present system is the attractive interaction between the particles and the surface, which instigates the periodicity of the particle deposition.
Adaptive Threshold Procedures: BUDTIF (1968)

Consideration of recent psychoacoustic research reveals that, independent of the general acceptance of the theory of signal detectability, threshold methodology continues to play a major rôle in the acquisition of psychoacoustic data. Although adaptive methods are widely used, the newer, finite-trial, adaptive methods are not—possibly owing to a misconception regarding the impossibility of obtaining psychometric function slopes and information other than threshold with such methods. The simplest of the finite-trial adaptive methods, the Block Up-and-Down, Two-Interval Forced-Choice (BUDTIF) method is investigated, and an attempt is made to show the feasibility and efficiency of obtaining such information with an adaptive method. Specifically, the variability and bias of repeated thresholds obtained using human subjects with two-, four-. and eight-trial block sizes and from 16 to 144 per threshold were determined. Results indicate that, for a target performance level of 75%, a block of four trials leads to minimal between-threshold variability. Although between-threshold variability is indirectly related to the number of trials per threshold, if greater precision is necessary it would seem preferable to invest the subject's time in more short threshold runs than fewer long threshold runs. An adaptive stopping rule is suggested.
Stabilization of oils by microencapsulation with heated protein‐glucose syrup mixtures (2006)

Abstract The use of proteins [whey protein isolate (WPI) or soy protein isolate (SPI) in combination with dried glucose syrup (DGS) for stabilization of microencapsulated spray‐dried emulsions containing tuna oil, palm stearin, or a tuna oil‐palm stearin blend was investigated. Pre‐emulsions containing heated (100°C/30 min) protein‐DGS mixtures and oils at oil/protein ratios of 0.75∶1 to 4.5∶1 were homogenized at two passes (35+10 or 18+8 MPa) and spray‐dried to produce 20–60% oil powders. Microencapsulation efficiency decreased at lower homogenization pressure and as the oil load in the powder was increased beyond 50% but was independent of the type of oil encapsulated and the total solids (TS) content of the emulsions (24–33% TS) prior to drying. Oxidative stabilities of the powders, as indicated by headspace propanal values and PV after 4 wk of storage at 23°C, generally decreased with increasing oil content and homogenization pressure but increased with increasing TS of the emulsion prior to drying. Powder containing palm stearin was more stable to oxidation than powders containing a 1∶1 ratio of palm stearin and tuna oil or only tuna oil. Heated WPI‐DGS formulations were superior to corresponding formulations stabilized by heated SPI‐DGS, producing spray‐dried powders with higher microencapsulation efficiency and superior oxidative stability.
Plasma carcinoembryonic antigen and acinar cell carcinoma of the pancreas (1984)

Seventeen patients with histologically proven pancreatic cancers were studied in order to clarify the relationship of histologic types to plasma carcinoembryonic antigen (CEA) values. Two cases with marked elevation of plasma CEA values having 6100 ng/ml and 2500 ng/ml, respectively, disclosed histologically acinar cell carcinoma and mixed acinar and ductal cell carcinoma, respectively. Despite of massive hepatic metastases, the other 15 cases with ductal cell carcinoma, including 3 cases with cystadenocarcinoma, adenoacanthoma, and undifferentiated pancreatic cancer, respectively, showed normal or very modest elevation of plasma CEA values. No correlation was obtained between plasma CEA values and several biochemical tests. Two patients with marked elevation of plasma CEA value revealed strong staining in the cancerous areas of the pancreas by using a peroxidase-antiperoxidase staining technique. These findings suggest that acinar cell carcinoma of the pancreas may contribute to increase the circulating plasma CEA value.
5-Substituted Pyrimidines with a 1,5-Anhydro-2,3-dideoxy-<scp>d</scp>-<i>arabino</i>-hexitol Moiety at N-1:  Synthesis, Antiviral Activity, Conformational Analysis, and Interaction with Viral Thymidine Kinase (1998)

A new series of anhydrohexitol nucleosides are described. These compounds have a pyrimidine base moiety substituted in the 5-position with a chloro (1b), trifluoromethyl (1c), vinyl (1d), 2-thienyl (1e), ethynyl (1f) or propynyl (1g) substituent. The vinyl, propynyl, and, in particular, the 5-trifluoromethyl analogue showed potent activity against herpes simplex virus (HSV), 1c with a selectivity index of >16000 against HSV-1 and >1000 against HSV-2. Conformational analysis of anhydrohexitol nucleosides using computational methods indicates that these nucleosides occur in an equilibrium between the C1 and 1C form with a DeltaE of 5.9 kJ/mol. When the anhydrohexitol nucleoside is cocrystallized with the HSV-1 thymidine kinase it adopts a 1C conformation, which is opposite to the conformation found for the small molecule alone. The enzyme, apparently, induces a conformational change, and conformational flexibility of an anhydrohexitol nucleoside may be advantageous for recognition by viral enzymes.
Can early malignant melanoma be differentiated from atypical melanocytic nevus by in vivo techniques? (1997)

Reliable differentiation between early MM and AMN with high sensitivity is possible using machine vision techniques to analyze digitized dermoscopic lesion images.
Genomic Computing. Explanatory Analysis of Plant Expression Profiling Data Using Machine Learning (2001)

“Actually, the orgy of fact extraction in which everybody is currently engaged has, like most consumer economies, accumulated a vast debt. This is a debt of theory, and some of us are soon going to have an exciting time paying it back—with interest, I hope.”

—Sydney Brenner, In Theory ,
Understanding Environmental Effect on Building Vibration for Structural Health Monitoring Using Event Detection and Causal Analysis (2013)

Structural damage diagnosis algorithms often involve analyzing vibration responses to extract information about dynamic characteristics closely related to integrity. The vibration data are, however, often influenced by various environmental effects, which may degrade diagnosis performance and result in erroneous decisions. This paper focuses on understanding the consequence of significant environmental effects, such as trains passing nearby, on building vibration data using event detection methods and causal analysis. The event detection methods identify significant events using wavelet analysis, which is effective for decomposing non-stationary signals. The causal analysis allows us to investigate wave propagation patterns in structures by quantifying causal dependencies between measurements collected from different locations using directed information. These methods are applied to acceleration data collected from 40 accelerometers deployed to an 11-story office building located next to railway. The results show clear patterns of causal dependencies among vibration data from different locations in the building, and their patterns change under different environmental conditions. It provides insights about environmental loading effects on building vibration that can be helpful for improving the accuracy of damage diagnosis
Implication of serum microRNA-7a/B with myocardial cell injury induced by ischemia reperfusion (2018)

Objective: To investigate the association between serum microRNA-7a/b and Myocardial Cell Injury (MCI) induced by ischemia reperfusion in Acute Myocardial Infarction (AMI) patients. Methods: Sixty (60) senile AMI patients were selected and placed in the observation group (A group), while 60 healthy people served as the healthy control group (group B). Depending on their conditions after emergency thrombolytic therapy, the AMI patients were sub-divided into no-reflow group (A1 group, 23 cases) and reperfusion group (A2 group, 37 cases). Blood levels of high-sensitive C-reactive protein (hs-CRP) and N-terminal pro-natriuretic peptide (NT-proBNP) were determined in all patients. MicroRNA-7a/b expressions were measured in venous blood 24 h and 120 h before and after thrombolytic therapy. Results: There were significant, time-dependent increases in microRNA-7a/b expression after thrombolytic therapy, when compared with the control group (p<0.05). Results of correlation analysis showed that microRNA-7a/b was positively correlated with hs-CRP (r1=0.666, p<0.05; but negatively correlated with D-D (r2=-0.642, p<0.05). Conclusion: In myocardial cell injury induced by ischemia reperfusion, microRNA-7a/b expression is linked to oxidative stress and apoptosis of cardiomyocytes. Thus I/RI might be mitigated by regulating the expression of this microRNA.