gebhart/patrepeval huggingface dataset:
Native HIV Type 1 Virion Surface Structures: Relationships between Antibody Binding and Neutralization or Lessons from the Viral Capture Assay (2004)

Despite a vigorous antibody response following HIV-1 infection, antibodies which neutralize primary isolates tend to be of low titer or sporadic. Similarly, antibodies produced in response to HIV-1 vaccines in human and animals react with HIV but, only on occasion, do these antibodies neutralize primary isolates. The failure of the immune system to respond in an effective manner is related to the inherent structural properties of the HIV-1 envelope expressed on the native virion and the pathogenesis of HIV infection. Identification of effective antibody interactions with HIV, as judged by inhibition of virus, is crucial for the development of broadly effective HIV vaccines and immune therapeutics. It has been proposed that antibodies must bind and neutralize virus to be effective at controlling HIV infection. We propose that this hypothesis may limit the identification of effective antibodies that are desperately needed given the difficulty in preventing and treating HIV. We provide evidence that the viral capture assay (VCA) is an important adjunct to the study of antibody interactions with primary isolate virus. Further, we propose that antibodies that are ineffective in traditional neutralization assays may also be effective at limiting viral spread and preventing viral infection.
Association of −344/T/C aldosterone synthase polymorphism (CYP11B2) with left ventricular structure and humoral parameters in young normotensive men (2004)

In agreement with previous studies, we found that the TT genotype of T-344C polymorphism of aldosterone synthase gene was associated with significantly higher levels of PRA in normotensive men. In subjects with high PRA, the TT genotype was associated with higher values of the LVMI.
How Do Enzymes Work? (1988)

The principle of transition-state stabilization asserts that the occurrence of enzymic catalysis is equivalent to saying that an enzyme binds the transition state much more strongly than it binds the ground-state reactants. An outline of the origin and gradual acceptance of this idea is presented, and elementary transition-state theory is reviewed. It is pointed out that a misconception about the theory has led to oversimplification of the accepted expression relating catalysis and binding, and an amended expression is given. Some implications of the transition-state binding principle are then explored. The amended expression suggests that internal molecular dynamics may also play a role in enzymic catalysis. Although such effects probably do not make a major contribution, their magnitude is completely unknown. Two examples of recent advances due to application of the transition-state binding principle are reviewed, one pertaining to the zinc protease mechanism and the other to the generation of catalytic antibodies.
Characterization of AlF_3 thin films at 193 nm by thermal evaporation (2005)

Aluminum fluoride (AlF3) was deposited by a resistive heating boat. To obtain a low optical loss and high laser-induced damage threshold (LIDT) at 193 nm, the films were investigated under different substrate temperatures, deposition rates, and annealing after coating. The optical property (the transmittance, refractive index, extinction coefficient, and optical loss) at 193 nm, microstructure (the cross-sectional morphology, surface roughness, and crystalline structure), mechanical property (stress), and LIDT of AlF3 thin films have been studied. AlF3 thin films deposited at a high substrate temperature and low deposition rate showed a lower optical loss. The highest LIDT occurred at the substrate temperature of 150 degrees C. The LIDT of the films prepared at a deposition rate of 2 A/s was higher than that at other deposition rates. The annealing process did not influence the optical properties too much, but it did increase the LIDT and stress.
Selective Precipitation of Proteins (2016)

Abstract Selective precipitation of proteins can be used as a bulk method to recover the majority of proteins from a crude lysate, as a selective method to fractionate a subset of proteins from a protein solution, or as a very specific method to recover a single protein of interest from a purification step. This unit describes a number of methods suitable for selective precipitation. In each of the protocols that are outlined, the physical or chemical basis of the precipitation process, the parameters that can be varied for optimization, and the basic steps for developing an optimized precipitation are described. © 2016 by John Wiley & Sons, Inc.
Investigation of Biodiesel Production from Canola Oil using Mg-Al Hydrotalcite Catalysts (2007)

Biodiesel produced by the transesterification of vegetable oils is a promising alternative fuel to diesel because of limited fossil fuel resources and environmental concerns. The use of heterogeneous catalysts greatly simplifies the technological process by facilitating the separation of the post-reaction mixture. The purpose of the present work was to examine a heterogeneous catalyst, in particular, Mg-Al hydrotalcites, to produce methyl esters of canola oil. In this study, the transesterification of canola oil with methanol was studied in a heterogeneous system, using Mg-Al hydrotalcites as solid base catalysts. The results showed that methanol is the best alcohol for this reaction condition. The highest triglyceride conversion rate of 71.9% was achieved after 9 h of reaction at 60 °C, with a 6:1 molar ratio of methanol to canola oil and a 3 wt% catalyst with 125-150 m m particles.
Does a glass of red wine improve endothelial function? (2000)

After ingestion of red wine with alcohol the brachial artery dilated and the blood flow increased. These changes were not observed following the de-alcoholized red wine and were thus attributable to ethanol. These haemodynamic changes may have concealed an effect on flow-mediated brachial artery dilatation which did not increase after drinking red wine with alcohol. Flow-mediated dilatation of the brachial artery increased significantly after de-alcoholized red wine and this finding may support the hypothesis that antioxidant qualities of red wine, rather than ethanol in itself, may protect against cardiovascular disease.
Welsh v. Wisconsin: A View from Counsel (1985)

the United States Supreme Court upheld Edward Welsh's claim that police could not, without consent and without a warrant, enter his home to arrest him for drunk driving, a nonjailable offense committed outside their presence.Justice Brennan, expressing the views of six Justices, rejected the claim that exigent circumstances allowed a warrantless nonconsensual home entry."[A]n important factor to be considered when determining whether any exigency exists is the gravity of the underlying offense for which the arrest is being made."' Home entries, continued the Court, "should rarely be sanctioned when there is probable cause to believe that only a minor offense . . .has been committed." 2 Margaret Satterthwaite and I were prevailing counsel in the Supreme Court and the result was, of course, pleasing.How this case got so far, how we became involved, and how fortuitous events, more than counsels' skills, produced the rarity of a recent Supreme Court opinion upholding a fourth amendment claim, is the subject of this article.Cases beginning in traffic courts seldom reach the Supreme Court.Indeed, the accidents and errors that led the case on that path are unusual.The issues stressed by Justice Brennan were not clearly presented to any of the three Wisconsin courts.Normally the Supreme Court does not grant review if the precise question was not thoroughly litigated below.
Metagenomics for the Discovery of Novel Human Viruses (2010)

Modern laboratory techniques for the detection of novel human viruses are greatly needed as physicians and epidemiologists increasingly deal with infectious diseases caused by new or previously unrecognized pathogens. There are many clinical syndromes in which viruses are suspected to play a role, but for which traditional microbiology techniques routinely fail in uncovering the etiologic agent. In addition, new viruses continue to challenge the human population owing to the encroachment of human settlements into animal and livestock habitats, globalization, climate change, growing numbers of immunocompromised people and bioterrorism. Metagenomics-based tools, such as microarrays and high-throughput sequencing are ideal for responding to these challenges. Pan-viral microarrays, containing representative sequences from all known viruses, have been used to detect novel and distantly-related variants of known viruses. Sequencing-based methods have also been successfully employed to detect novel viruses and have the potential to detect the full spectrum of viruses, including those present in low numbers.
Polarisation-insensitive travelling-wave electrodeelectroabsorption (TW-EA)modulator with bandwidth over 50 GHz and driving voltage less than 2 V (1997)

The proposed TW-EA modulator has a thin intrinsic layer (a 0.2 µm thick strained InGaAlAs (13 nm)/InAlAs (5 nm) MQW) and short interaction length (200 µm). The optical 3 dB modulation bandwidth exceeds 50 GHz, and the driving voltages for the 15 dB extinction ratio are 1.7 and 1.9 V for TE and TM modes respectively, at 1.55 µm wavelength.
Wide Dispersion of ST175 Clone despite High Genetic Diversity of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Clinical Strains in 16 Spanish Hospitals (2011)

During the COMParative Activity of Carbapenems Testing (COMPACT) surveillance study, 448 Pseudomonas aeruginosa clinical isolates were obtained from 16 Spanish hospitals. Nonsusceptibility (EUCAST breakpoints) to imipenem (35%), meropenem (33%), and/or doripenem (33%) was observed with 175 isolates (39%). Simultaneous resistance to these three drugs was observed with 126 of the 175 isolates (72%). Except for colistin, high resistance rates were observed among noncarbapenem antibiotics. Clonal relatedness was investigated by pulsed-field gel electrophoresis (PFGE) with SpeI, discriminating 68 patterns. Multilocus sequence typing (MLST) was performed on 84 isolates representing different PFGE types and all participating hospitals. Thirty-nine sequence types (STs) could be distinguished, and of these, ST175 (48 isolates, 10 hospitals), ST646 (16 isolates, 4 hospitals), ST532 (13 isolates, 3 hospitals), and ST111 (13 isolates, 7 hospitals) were the most frequently encountered. Minimum-spanning tree analysis confirmed a wide dissemination of different clones among participant hospitals, particularly ST175. PFGE pattern comparison within the four most frequent STs revealed that ST175 isolates were relatively uniform, while ST646, ST532, and ST111 isolates were highly diverse, with almost every isolate belonging to a unique pulsotype, even when originating from the same center. The population of carbapenem-nonsusceptible P. aeruginosa isolates from 16 hospitals is highly diverse, with one ST (ST175) representing a highly conserved clone disseminated in 10 of the 16 participant hospitals. This ST175 clone should be added to the list of P. aeruginosa clones at high risk for epidemic spread, such as the Liverpool, Manchester, and Melbourne clones previously found in cystic fibrosis patients and ST235 in the nosocomial setting.
Reversible Aphasia in Adolescence: A Late-Onset form of Landau Kleffner Syndrome? Report of a Single Case (1997)

An adolescent boy developed a long-lasting pattern of global aphasia, concomitant to focal (left temporal) EEG abnormalities; this was followed by complete recovery. Laboratory and neuroimaging studies were within normal limits. The possibility of a late-onset Landau Kleffner syndrome is discussed.
Blind Source Separation Combining Simo-Ica and Simo-Model-Based Binary Masking (2006)

A new two-stage blind source separation (BSS) for convolutive mixtures of speech is proposed, in which a single-input multiple-output (SIMO)-model-based ICA and a new SIMO-model-based binary mask processing are combined. SIMO-model-based ICA can separate the mixed signals, not into monaural source signals but into SIMO-model-based signals from independent sources as they are at the microphones. Thus, the separated signals of SIMO-model-based ICA can maintain the spatial qualities of each sound source. Owing to the attractive property, novel SIMO-model-based binary mask processing can be applied to efficiently remove the residual interference components after SIMO-model-based ICA. The experimental results reveal that the separation performance can be considerably improved by using the proposed method compared with the conventional BSS methods
Genetics and geometry of canalization and developmental stability in Drosophila subobscura (2005)

The results strongly support the hypothesis that environmental canalization and developmental stability share underlying regulatory mechanisms, but environmental and genetic canalization are not functionally the same. A likely explanation for this lack of association is that natural wing shape variation in Drosophila populations is loosely related to individual fitness.
DCDB: Drug combination database (2009)

Rapid advances in pharmaceutical sciences have brought ever-increasing interests in combined therapies for better clinical efficacy and safety, especially in cases of complicated and refractory diseases. Innovative experimental technologies and theoretical frameworks are being actively developed for multicomponent drug research. In this work, we present the Drug Combination Database, with aims to facilitate analyses of known drug combinations, to summarize patterns of beneficial drug interactions, and to provide a basis for theoretical modeling and simulation of such drug interactions. Its current version (1.0) collected 499 approved or investigational drug combinations, including 40 unsuccessful drug combinations, involving 485 individual drugs, from >6000 references.
Guaiacol -- a new compound in the treatment of gastro-oesophageal reflux? (1982)

The effects on the oesophagus of an aromatic oil, guaiacol, has been examined in a group of 20 patients with reflux oesophagitis and also normal volunteers. This agent produced a rapid and sustained rise in resting lower oesophageal sphincter pressures and the peristaltic pressures induced in response to swallowing liquids. This compound may prove useful in the treatment of patients with reflux oesophagitis and other disorders of oesophageal motility.
The Role of Early Life Environmental Risk Factors in Parkinson Disease: What Is the Evidence? (2005)

Parkinson disease (PD) is of unknown but presumably multifactorial etiology. Neuropathologic studies and animal models show that exposure to environmental neurotoxicants can determine progressive damage in the substantia nigra many years before the onset of clinical parkinsonism. Therefore, PD, like other neurologic diseases related to aging, may be determined by exposures present in the environment early during the life span or even during pregnancy. Recent epidemiologic studies have focused on the possible role of environmental risk factors present during adult life or aging. Smoking and coffee drinking have consistently been identified to have protective associations, whereas roles of other risk factors such as pesticide and infections have been reported in some studies but not replicated in others. Both genetic inheritance and sharing of common environment in the same family explain the increased risk of PD of relatives of PD cases compared with relatives of controls in familial aggregation studies. Much evidence indicates that risk factors that have a long latency or a slow effect could be important for late-onset PD. Further epidemiologic studies are warranted in this area.
Mortality in a cohort of vermiculite miners exposed to fibrous amphibole in Libby, Montana (2004)

The all-cause linear model would imply a 14% increase in mortality for mine workers exposed occupationally to 100 f/ml.y or about 3.2% for a general population exposed for 50 years to an ambient concentration of 0.1 f/ml. Amphibole fibres, tremolite in particular, are likely to be disproportionately responsible for cancer mortality in persons exposed to commercial chrysotile, but to what extent cannot be readily assessed.
A data parallel programming model based on distributed objects (2003)

This paper proposes a data parallel programming model suitable for loosely synchronous, irregular applications. At the core of the model are distributed objects that express non-trivial data parallelism. Sequential objects express independent computations. The goal is to use objects to fold synchronization into data accesses and thus, free the user from concurrency aspects. Distributed objects encapsulate large data partitioned across multiple address spaces. The system classifies accesses to distributed objects as read and write. Furthermore, it uses the access patterns to maintain information about dependences across partitions. The system guarantees inter-object consistency using a relaxed update scheme. Typical access patterns uncover dependences for data on the border between partitions. Experimental results show that this approach is highly usable and efficient.
Posterior Lumbar Interbody Fusion with Specialized Instruments (1985)

Posterior lumbar interbody fusion (PLIF) has been performed in 100 individuals by use of specialized surgical instruments and allogeneic preserved bone grafts from 1979 to March 1982, after the advantages of performing PLIF in 342 individuals from 1965 to 1978 were noted. No deaths occurred, nor any infections or thrombophlebitis postoperation. Eleven (11%) reoperations were required: six for proven pseudarthrosis, three for gradual bone graft extrusion (of six extrusions total), one for bone graft fracture (with manifestations of nerve root compression), and one for hematoma. Operative results were excellent in 35%, good in 39%, fair in 17%, and poor in 9%. Specialized surgical instruments used for the operation included mortising chisels with cannulated reamers, right-angled curettes, and depth-limited impactors. PLIF is technically demanding; however, it establishes a mortise-graft interbody fusion to stabilize and restore the spinal architecture.
Histone deacetylase inhibitors impair NK cell viability and effector functions through inhibition of activation and receptor expression (2011)

HDACi are being used as a novel, therapeutic approach for leukemias and other hematological malignancies. However, their effect on immune cells remains ill-defined, as HDACi may impair immune surveillance. In this work, we demonstrate that TSA, VPA, and NaB inhibited IFN-γ production by CD56(dim) and CD56(bright) NK cells and NK cell-mediated cytotoxicity against K562 target cells. HDACi promoted minor NK cell apoptosis but inhibited nuclear mobilization of NF-κB p50, which was accompanied by a robust down-regulation of NKG2D and NKp46 on resting NK cells and of NKG2D, NKp44, NKp46, and CD25 on cytokine-activated NK cells. Decreased CD25 expression promoted a weakened IFN-γ secretion upon restimulation of NK cells with IL-2, whereas reduced expression of NKG2D and NKp46 was accompanied by an impaired NKG2D- and NKp46-dependent cytotoxicity. Moreover, NK cells from normal mice treated in vivo with TSA displayed a diminished expression of NK1.1, NKG2D, and NKp46 and secreted reduced amounts of IFN-γ upon ex vivo stimulation with cytokines. Thus, our preclinical results indicate that HDACi exert deleterious effects on NK cell function, which may weaken immune surveillance and facilitate relapse of the malignant disease in HDACi-treated patients.
<title>Retrieval of multi- and hyperspectral images using an interactive relevance feedback form of content-based image retrieval</title> (2001)

This paper demonstrates the capability of a set of image search algorithms and display tools to search large databases for multi- and hyperspectral image cubes most closely matching a particular query cube. An interactive search and analysis tool is presented and tested based on a relevance feedback approach that uses the human-in-the-loop to enhance a content-based image retrieval process to rapidly find the desired set of image cubes.
Maternal allergen immunization during pregnancy in a mouse model reduces adult allergy‐related antibody responses in the offspring (2002)

Maternal allergen immunization might favour selection for an allergen-specific Th1-dependent antibody response in the offspring. Our results indicate that IgE suppression is stronger after maternal allergen exposure during early pregnancy than after exposure in late pregnancy.
Through-process modeling for design-for-manufacturability applications (2007)

In recent years, design for manufacturability (DFM) has become an important focus item of the semiconductor industry and many new DFM applications have arisen. Most of these applications rely heavily on the ability to model process sensitivity, and here we explore the role of through-process modeling on DFM applications. Several different DFM applications are examined and their lithography model requirements analyzed. The complexities of creating through-process models are then explored, and methods to ensure their accuracy presented.
Doxorubicin-induced skin ulcer in the piglet. (1983)

Skin ulceration produced by inadvertently extravasated doxorubicin is characterized by a prolonged course accompanied by severe morbidity, and it has proven to be notoriously difficult to treat. In attempts to identify possible antidotes, 11 different pharmacologic agents were tested using piglets, because their skin is anatomically similar to that of man. Among the agents studied, topical application of DMSO daily for 7 days tended to decrease the maximal diameter and accelerate healing of skin ulcers produced by intradermal doxorubicin. alpha-Tocopherol appeared to worsen the ulceration. None of the 11 agents studied prevented the development of ulcerations completely.
A multi-level middle-out cross-zooming approach for large graph analytics (2009)

This paper presents a working graph analytics model that embraces the strengths of the traditional top-down and bottom-up approaches with a resilient crossover concept to exploit the vast middle-ground information overlooked by the two extreme analytical approaches. Our graph analytics model is co-developed by users and researchers, who carefully studied the functional requirements that reflect the critical thinking and interaction pattern of a real-life intelligence analyst. To evaluate the model, we implement a system prototype, known as GreenHornet, which allows our analysts to test the theory in practice, identify the technological and usage-related gaps in the model, and then adapt the new technology in their work space. The paper describes the implementation of GreenHornet and compares its strengths and weaknesses against the other prevailing models and tools.