gebhart/patrepeval huggingface dataset:
Treatment of Experimental Anterior and Intermediate Uveitis by a Dexamethasone Intravitreal Implant (2011)

A single administration of DEX implant significantly reduced inflammation in an animal model of anterior and intermediate uveitis.
Radio-frequency heating and current drive experiments on the Princeton Large Torus (1984)

In all instances described, H-Y antigen was found when testes were present. Extragonadal tissues in androgen-insensitive individuals with TFS were typed H-Y+, indicating that this cell surface component is hormone-independent. Thus, association of H-Y antigen and primary sex determination is reinforced. But variation in the degree of masculinization observed in certain mammalian intersexes (e.g., polled goats) is not explained by simple H-Y antigen dosage effects. Additional genetic and/or intrauterine modifiers may influence both gonadal and somatic tissue target cell sensitivity to hormones.
Chemical Abstracts material on‐line (1979)

Chemical Abstracts Issues and Indexes have been available in printed form since 1907. Microform versions are also available now. In the near future Chemical Abstracts material will be accessible by computer in the UK via six on‐line systems and one batch current awareness system. This variety of modes of access is further diversified by the variety of ways in which the original Chemical Abstracts Service (CAS) files have been implemented for use with the different search systems, and by the differences in the system facilities, pricing structure and technical back‐up offered by the service suppliers. This paper attempts to bring together in tabular form factors which should be considered in taking rational decisions on how to get the ‘best’ out of Chemical Abstracts material, the ‘best’ being the optimum performance/cost ratio for any given topic.
Circular and Thin-Wall Torsion (2012)

Abstract This chapter introduces the fundamental kinematic assumption associated with the torsion of circular bars. It treats the equilibrium of twisted rods and examines the behaviour of elastic as well as plastically deformed bars. Both physical as well as differential equation approaches are used as are elementary conservation of energy ideas. Torsional failure of brittle and ductile materials is presented. For non-circular geometries, the concept of thinness is exploited to develop the theory of torsion of thin-walled tubes. The concepts of shear flow are developed for stress analysis, and energy conservation is utilized to understand kinematic response.
Influences of Density on Circular Clarifiers with Baffles (1992)

The effects of the inlet densimetric Froude number on the velocity and suspended solids concentration fields in secondary circular clarifiers are investigated by application of a verified numerical model. The model consists of a set of conservation equations for continuity and momentum, turbulent kinetic energy k, dissipation of turbulence energy E, and solids concentration. The densimetric Froude number as determined from typical tank geometry, solids loading and flow, varied from 0.078 to 1.052. The inlet density waterfall was studied to determine its effect on the settling zone flow pattern and tank performance. It was found, in both physical and numerical models, that the density waterfall entrained large volumes of the ambient fluid. The entrainment compensating flow rate increased inversely with the densimetric Froude number. The strength of the bottom density current, the upward flow in the withdrawal zone, and the recirculation all increased with a decreasing densimetric Froude number, largely due to the entrainment into the density waterfall. The increase in the upward flow in the withdrawal zone resulted in a degradation in the clarifier performance. There was generally good agreement between the model simulations and available field measurements and physical model data.
Nanolithographic control of carbon nanotube synthesis (2009)

A method offering precise control over the synthesis conditions to obtain carbon\nnanotube (CNT) samples of a single chirality (metallic or semi-conducting) is presented.\nUsing this nanolithographic method of catalyst deposition, the location of CNT growth is\nalso precisely defined.\nThis technique obviates three significant hurdles that are preventing the exploitation\nof CNT in micro- and nano-devices. Microelectronic applications (e.g., interconnects,\nCNT gates, etc.) require precisely defined locations and spatial density, as well as\nprecisely defined chirality for the synthesized CNT. Conventional CVD synthesis\ntechniques typically yield a mixture of CNT (semi-conducting and metallic types) that\ngrow at random locations on a substrate in high number density, which leads to extreme\ndifficulty in application integration.\nDip Pen Nanolithography (DPN) techniques were used to deposit the catalysts at\nprecisely defined locations on a substrate and to precisely control the catalyst\ncomposition as well as the size of the patterned catalyst. After deposition of catalysts, a\nlow temperature Chemical Vapor Deposition (CVD) process at atmospheric pressure\nwas used to synthesize CNT. Various types of catalysts (Ni, Co, Fe, Pd, Pt, and Rh) were\ndeposited in the form of metal salt solutions or nano-particle solutions. Various characterization studies before and after CVD synthesis of CNT at the location of the\ndeposited catalysts showed that the CNT were of a single chirality (metallic or semiconducting)\nas well as a single diameter (with a very narrow range of variability).\nAdditionally, X-ray photoelectron spectroscopy (XPS) was used to characterize the\ndeposited samples before and after the CVD, as was lateral force microscopy (LFM) for\ndetermination of the successful deposition of the catalyst material immediately after\nDPN as well as following the CVD synthesis of the samples. The diameter of the CNT\ndetermines the chirality. The diameter of the CNT measured by TEM was found to be\nconsistent with the chirality measurements obtained from Raman Spectroscopy for the\ndifferent samples. Hence, the results showed that CNT samples of a single chirality can\nbe obtained by this technique. The results show that the chirality of the synthesized CNT\ncan be controlled by changing the synthesis conditions (e.g., size of the catalyst patterns,\ncomposition of the catalysts, temperature of CVD, gas flow rates, etc.).
Inactivation of Surface-Borne Microorganisms and Increased Germination of Seed Specimen by Cold Atmospheric Plasma (2013)

Sustaining the quality of seeds is a major task in attempting to supply nutrition to the growing world population. In this study, the seeds of Cicer arietinum were exposed to cold atmospheric plasma (CAP). A significant reduction of the natural microbiota attached to the seed surface was observed for increasing CAP treatment times-2 and 5 min were sufficient to achieve a 1 and 2 log reductions, respectively. Furthermore a 1 min CAP treatment showed a strongly improved seed germination (89.2 %), speed of germination (7.10.1 seeds/day), and increased seed vigor, beside a decrease in the mean germination time (2.7 days) compared with controls. The roughness profile of the seed cotyledon was altered significantly, only in case of longer treatment times from 5 min. These results suggest that CAP technology has the potentiality to reduce health risks associated with contaminated seeds, while improving food quality.
Validation of three-dimensional simulation method for two-phase flow in triangular-pitch tube bundle in secondary side of steam generators on porous two-fluid model (2021)

In the design process of a steam generator, a porous-media-approach computational code is utilized for simulating three-dimensional two-phase flow behavior in the secondary side of steam generators. For the design of next-generation steam generators, the advanced thermal-hydraulic analysis code based on the two-fluid model has been developed by implementing constitutive equations into the ANSYS fluent. For code validation, experiments using two-phase simulant fluids were performed to collect data in a simulated steam generator with a triangular tube array. The simulant two-phase flow system selected in the experiment was an adiabatic sulfur hexafluoride gas and liquid ethanol system, which allowed us to achieve the density ratio of prototypic steam-water flow with low pressure (=0.68 MPa). In the experiment, void fraction and gas–liquid interfacial velocity distributions along U-tubes were measured. The code validation was conducted by analyzing code predictions for measured distributions of void fraction and interfacial velocity under prototypic full load and partial load conditions, i.e., 50–80% flow rate conditions. Their bias and random errors were evaluated. The reasonable random errors demonstrated the validity of the newly developed code based on the two-fluid model in terms of predictions of void fraction and interfacial velocity in the secondary side of steam generators.
Inhibitors of Rho kinase (ROCK) signaling revert the malignant phenotype of breast cancer cells in 3D context (2016)

Loss of polarity and quiescence along with increased cellular invasiveness are associated with breast tumor progression. ROCK plays a central role in actin-cytoskeletal rearrangement. We used physiologically relevant 3D cultures of nonmalignant and cancer cells in gels made of laminin-rich extracellular matrix, to investigate ROCK function. Whereas expression levels of ROCK1 and ROCK2 were elevated in cancer cells compared to nonmalignant cells, this was not observed in 2D cultures. Malignant cells showed increased phosphorylation of MLC, corresponding to disorganized F-actin. Inhibition of ROCK signaling restored polarity, decreased disorganization of F-actin, and led to reduction of proliferation. Inhibition of ROCK also decreased EGFR and Integrinβ1 levels, and consequently suppressed activation of Akt, MAPK and FAK as well as GLUT3 and LDHA levels. Again, ROCK inhibition did not inhibit these molecules in 2D. A triple negative breast cancer cell line, which lacks E-cadherin, had high levels of ROCK but was less sensitive to ROCK inhibitors. Exogenous overexpression of E-cadherin, however, rendered these cells strikingly sensitive to ROCK inhibition. Our results add to the growing literature that demonstrate the importance of context and tissue architecture in determining not only regulation of normal and malignant phenotypes but also drug response.
Selective Logging in the Brazilian Amazon (2005)

Amazon deforestation has been measured by remote sensing for three decades. In comparison, selective logging has been mostly invisible to satellites. We developed a large-scale, high-resolution, automated remote-sensing analysis of selective logging in the top five timber-producing states of the Brazilian Amazon. Logged areas ranged from 12,075 to 19,823 square kilometers per year (+/-14%) between 1999 and 2002, equivalent to 60 to 123% of previously reported deforestation area. Up to 1200 square kilometers per year of logging were observed on conservation lands. Each year, 27 million to 50 million cubic meters of wood were extracted, and a gross flux of approximately 0.1 billion metric tons of carbon was destined for release to the atmosphere by logging.
Effects of amoxicillin-clavulanate combination on the motility of the small intestine in human beings (1991)

The amoxicillin-clavulanate combination (Augmentin) frequently induces gastric complaints and diarrhea by an unknown mechanism. The aim of this study was to assess the effects of two orally therapeutic regimens of amoxicillin-clavulanate on small bowel motility in human beings. Duodeno-jejunal manometric recordings were performed in six healthy subjects treated in a cross-over double-blind study with placebo; amoxicillin-clavulanate, 1 g plus 250 mg per os every 12 h for 3 days; or amoxicillin-clavulanate, 1 g plus 250 mg per os every 12 h on day 3 only (1-day regimen). Recordings were all performed on day 3 during a diurnal fasting period, a fed state after a standard dinner, and a nocturnal fasting period. Amoxicillin-clavulanate did not affect the motility of the small intestine during the diurnal fast or the fed state. During the nocturnal fast, amoxicillin-clavulanate significantly increased the motility index of the nonpropagated contractions and tended to increase the duration and the amplitude of the propagated contractions. The same digestive motor effect was already observed on the first day of treatment (1-day regimen). This study demonstrates that the oral administration of a therapeutic regimen of amoxicillin-clavulanate is associated, in most cases, with the occurrence of small intestinal motor disturbances.
Fraction genome altered (FGA) to regulate both cell autonomous and non-cell autonomous functions in prostate cancer and its effect on prostate cancer aggressiveness. (2020)

347 Background: Our ability to distinguish lethal from non-lethal forms of prostate cancer (PC) is limited. Given prostate tumors’ genetic heterogeneity, is it unlikely that a single somatic variant is prognostic. Herein we investigated fraction of genome altered (FGA; percentage of copy number altered chromosome regions out of measured regions; cBioportal) and tumor mutational count (TMC; number of mutational events per case) harbored by the primary tumor as two tumor-specific factors posited to influence disease aggressiveness or responsiveness to certain therapeutic agents. Methods: We used the TCGA data (n= 490 primary PC) and MSKCC-IMPACT (n=717, Zehir et al 2017) PC datasets to analyze the correlation between FGA and TMC in PC. GSEA was performed with transcriptomes used to identify signaling pathways associated with these two measures. We then categorized 490 primary PC patients from TCGA dataset into 4 groups based on FGA and TMC levels (based on the median values) to assess associations with outcomes. Results: Primary PC patients who harbor FGA high TMC low exhibited shorter disease-free survival (High Risk). We observed attenuation of the androgen signaling pathway and induction of cell proliferation pathways associated with this aggressive form of disease. We used results from CIBERSORT algorithm and deep learning methods of TCGA data and observed that quantities of tumor infiltrating lymphocytes was higher in the FGA high TMC low group (p=0.038). However, we also observed significantly reduced immune effector signaling-pathway signaling in this high-risk FGA high TMC low group suggesting the presence of immune-suppressive networks in primary disease associated with a high risk of progression. Conclusions: A greater understanding of molecular features of aggressive primary PC (FGA/TMC) will be important in developing management strategies. Based on our preliminary analyses, we hypothesize that patients whose primary PC harbors FGA high TMC low have a higher likelihood of aggressive disease due to their impact on PC cell proliferation and dedifferentiation (cell autonomous), and subdued immune responses (non-cell-autonomous).
Measurement of wavelength-dependent radiation pressure from photon reflection and absorption due to thin film interference (2018)

Opto-mechanical forces result from the momentum transfer that occurs during light-matter interactions. One of the most common examples of this phenomenon is the radiation pressure that is exerted on a reflective surface upon photon reflection. For an ideal mirror, the radiation pressure is independent of the wavelength of light and depends only on the incident power. Here we consider a different regime where, for a constant input optical power, wavelength-dependent radiation pressure is observed due to coherent thin film Fabry-Perot interference effects. We perform measurements using a Si microcantilever and utilize an in-situ optical transmission technique to determine the local thickness of the cantilever and the light beam's angle of incidence. Although Si is absorptive in the visible part of the spectrum, by exploiting the Fabry-Perot modes of the cantilever, we can determine whether momentum is transferred via reflection or absorption by tuning the incident wavelength by only ~20 nm. Finally, we demonstrate that the tunable wavelength excitation measurement can be used to separate photothermal effects and radiation pressure.
Quantitative assessment of chemical artefacts produced by propionylation of histones prior to mass spectrometry analysis (2016)

Histone PTMs play a crucial role in regulating chromatin structure and function, with impact on gene expression. MS is nowadays widely applied to study histone PTMs systematically. Because histones are rich in arginine and lysine, classical shot-gun approaches based on trypsin digestion are typically not employed for histone modifications mapping. Instead, different protocols of chemical derivatization of lysines in combination with trypsin have been implemented to obtain "Arg-C like" digestion products that are more suitable for LC-MS/MS analysis. Although widespread, these strategies have been recently described to cause various side reactions that result in chemical modifications prone to be misinterpreted as native histone marks. These artefacts can also interfere with the quantification process, causing errors in histone PTMs profiling. The work of Paternoster V. et al. is a quantitative assessment of methyl-esterification and other side reactions occurring on histones after chemical derivatization of lysines with propionic anhydride [Proteomics 2016, 16, 2059-2063]. The authors estimate the effect of different solvents, incubation times, and pH on the extent of these side reactions. The results collected indicate that the replacement of methanol with isopropanol or ACN not only blocks methyl-esterification, but also significantly reduces other undesired unspecific reactions. Carefully titrating the pH after propionic anhydride addition is another way to keep methyl-esterification under control. Overall, the authors describe a set of experimental conditions that allow reducing the generation of various artefacts during histone propionylation.
User Experience Design for E-Voting: How mental models align with security mechanisms (2019)

This paper presents a mobile application for vote-casting and vote-verification based on the Selene e-voting protocol and explains how it was developed and implemented using the User Experience Design process. The resulting interface was tested with 38 participants, and user experience data was collected via questionnaires and semi-structured interviews on user experience and perceived security. Results concerning the impact of displaying security mechanisms on UX were presented in a complementary paper. Here we expand on this analysis by studying the mental models revealed during the interviews and compare them with theoretical security notions. Finally, we propose a list of improvements for designs of future voting protocols.
Native Xquery processing in oracle XMLDB (2005)

With XQuery becoming the standard language for querying XML, and the relational SQL platform being recognized as an important platform to store and process XML, the SQL/XML standard is integrating XML query capability into the SQL system by introducing new SQL functions and constructs such as XMLQuery() and XMLTable. This paper discusses the Oracle XMLDB XQuery architecture for supporting XQuery in the Oracle ORDBMS kernel which has the XQuery processing tightly integrated with the SQL/XML engine using native XQuery compilation, optimization and execution techniques.
Dutch Elm Disease, a Model Tree Disease for Biological Control* (2020)

Dutch elm disease is the most widely known plant disease in the western world. It also is the most intensively studied tree disease and a prime example of a disease for which virtually every approach for control has been pursued. The story of Dutch elm disease thus represents a model for vascular diseases, as the life cycle of the pathogen is known in ever increasing detail, and transmittance of the disease is by vectors or root contact. Also, artificial infection of the host is simple, and trees having various degrees of resistance are known. Each one aims at a seemingly vulnerable spot in the complex relationship existing between the fungus, the beetles, and the susceptible elm species. Quarantines can theoretically exclude Dutch elm disease from an area, provided that there are elm-free natural barriers. In the experiments on biological control with Trichoderma, which is not known to produce any antibiotics, protective effects were observed after preventive treatments.
Correction: The Plasmodium falciparum STEVOR Multigene Family Mediates Antigenic Variation of the Infected Erythrocyte (2011)

Modifications of the Plasmodium falciparum-infected red blood cell (iRBC) surface have been linked to parasite-associated pathology. Such modifications enable the parasite to establish long-lasting chronic infection by evading antibody mediate immune recognition and splenic clearance. With the exception of the well-demonstrated roles of var-encoded PfEMP1 in virulence and immune evasion, the biological significance of other variant surface antigens (rif and stevor) is largely unknown. While PfEMP1 and RIFIN have been located on the iRBC surface, recent studies have located STEVOR at the iRBC membrane where it may be exposed on the erythrocyte surface. To investigate the role of STEVOR in more detail, we have developed antibodies against two putative STEVOR proteins and used a combination of indirect immunofluorescence assays (IFA), live IFA, flow cytometry, as well as agglutination assays, which enable us to demonstrate that STEVOR is clonally variant at the surface of schizont stage parasites. Crucially, expression of different STEVOR on the surface of the iRBC changes the antigenic property of the parasite. Taken together, our data for the first time demonstrate that STEVOR plays a role in creating antigenic diversity of schizont stage parasites, thereby adding additional complexity to the immunogenic properties of the iRBC. Furthermore, it clearly demonstrates that to obtain a complete understanding of how parasite-induced pathology is linked to variation on the surface of the iRBC, focusing the interactions of multiple multigene families needs to be considered.
Detection of intact megaDalton protein assemblies of vanillyl‐alcohol oxidase by mass spectrometry (2000)

Well-resolved ion signals of intact large protein assemblies, with molecular masses extending above one million Dalton, have been detected and mass analyzed using electrospray ionization mass spectrometry, with an uncertainty in mass of <0.2%. The mass spectral data seem to reflect known solution-phase behavior of the studied protein assembly and have therefore been directly used to probe the protein assembly topology and stability as a function of ionic strength and pH.
Topological distribution of four-alpha-helix bundles. (1989)

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts.