gebhart/patrepeval huggingface dataset:
Biofilm-induced calcium carbonate precipitation : application in the subsurface (2014)

Subsurface leakage mitigation strategies using ureolytic biofilm- or microbially-induced calcium carbonate precipitation (MICP) have been investigated for sealing high permeability or fractured regions. In the subsurface, this technology may help reduce unwanted preferential flow pathways thereby improving the storage security of geologically-stored carbon dioxide or sealing fractures caused by hydraulic fracturing. MICP has been researched for other applications, such as consolidating porous materials, improving construction materials and remediating environmental concerns. Injection strategies to control saturation conditions and region-specific precipitation were developed in sand-filled columns. Sporosarcina pasteurii biofilms were established and calcium and urea solutions were injected to promote mineralization. These injection strategies resulted in (1) promoting homogeneous distribution of CaCO 3 along the flow path, (2) minimizing near-injection point plugging, and (3) promoting efficient precipitation by reviving ureolytic activity. Additionally, a Darcy-scale model was calibrated and used to predict experimental results. The developed injection strategies were used to repeatedly seal a hydraulically fractured, 74 cm diameter Boyles Sandstone core under ambient pressures. To study meso-scale samples under relevant subsurface pressure conditions, a high pressure test vessel, rated to pressures of 96 bar, was developed. The hydraulically fractured sandstone core was loaded into the vessel and treated with MICP at 44 bar of confining pressure. After treatment, the permeability was reduced and the sandstone core withstood three times higher well bore pressures before re-fracturing compared to before MICP treatment. Additionally, MICP was promoted in three 2.5 cm diameter Berea Sandstone cores under 76 bar of pressure. The cores' permeabilities were reduced and their minimum capillary displacement pressures (MCDP) were increased. Exposure of the biomineralized cores to 24 hours of supercritical CO 2 did not negatively impact the permeability or MCDP achieved after mineralization. These studies suggest MICP may potentially seal and strengthen subsurface high permeability regions or fractures with the advantage that MICP technologies use low-viscosity fluids to penetrate small aperture pores that may not be reachable by traditional cement-based sealing technologies. These studies also point to the need for further research and development activities, particularly under subsurface relevant pressure conditions.
Adhesion formation to the uterine horn of the rat in response to nylon and a new absorbable clip. (1987)

We have evaluated the tissue reactivity as manifested by adhesion formation to the uterine horn of the rat in response to a new absorbable surgical clip. A standard lesion on the uterine horn was created and repaired with either nylon sutures or an absorbable clip. Adhesion formation to the operative site was evaluated using a point based grading system, seven, 21 and 120 days postoperatively. A statistically significant increase in adhesion formation and their severity was seen on the uterine horns repaired with the surgical clips. The adhesions did not improve with time. In two instances, abscesses were formed around the clips. The use of the surgical clips in the peritoneal cavity needs to be investigated further. Their use in women in the reproductive age group who wish to preserve their reproductive potential is discouraged.
A Machine Learning Approach to Foreign Key Discovery. (2009)

We study the problem of automatically discovering semantic associations between schema elements, namely foreign keys. This problem is important in all applications where data sets need to be integrated that are structured in tables but without explicit foreign key constraints. If such constraints could be recovered automatically, querying and integrating such databases would become much easier. Clearly, one may find candidates for foreign key constraints in a given database instance by computing all inclusion dependencies (IND) between attributes. However, this set usually contains many false positives due to spurious set inclusions. We present a machine learning approach to tackle this problem. We first compute all INDs of a given schema and let each be judged by a binary classification algorithm using a small set of features that can be derived efficiently using standard SQL. We demonstrate the feasibility of this approach using crossvalidation with several state-of-the-art classification algorithms. With the J48 algorithm, our approach consistently reaches F-measures above 80 % and often close to 100 % as evaluated on six different data sets from three different domains. 1.
Lipid Removal from Human Serum Samples (2000)

The efficacy of lipid removal from human serum samples obtained by using Cleanascite HC, a commercially available product, was compared to that obtained by the standard chloroform method. Separate samples of 21 frozen, banked human serum samples used in the preparation of samples for proficiency testing were treated with either Cleanascite HC or chloroform. The lipid content was measured before and after treatment. The total percentages of lipid removed ranged from 61 to 70% with Cleanascite HC and from 60 to 62% with chloroform. The advantage of Cleanascite HC over chloroform is based on the simplicity of the procedure with Cleanascite HC without the environmental concerns inherent in the use of chloroform. In 15 serum samples known to contain antibodies to treponemal and nontreponemal syphilis antigens, Cleanascite HC bound some immunoglobulin, but with only minimal loss of reactivity in the serologic tests for syphilis. Cleanascite HC is therefore an acceptable alternative to chloroform for lipid reduction in human serum samples.
An accurate cost model for guiding data locality transformations (2005)

Caches have become increasingly important with the widening gap between main memory and processor speeds. Small and fast cache memories are designed to bridge this discrepancy. However, they are only effective when programs exhibit sufficient data locality.The performance of the memory hierarchy can be improved by means of data and loop transformations. Tiling is a loop transformation that aims at reducing capacity misses by shortening the reuse distance. Padding is a data layout transformation targeted to reduce conflict misses.This article presents an accurate cost model that describes misses across different hierarchy levels and considers the effects of other hardware components such as branch predictors. The cost model drives the application of tiling and padding transformations. We combine the cost model with a genetic algorithm to compute the tile and pad factors that enhance the program performance.To validate our strategy, we ran experiments for a set of benchmarks on a large set of modern architectures. Our results show that this scheme is useful to optimize programs' performance. When compared to previous approaches, we observe that with a reasonable compile-time overhead, our approach gives significant performance improvements for all studied kernels on all architectures.
Human papillomavirus typing and DNA ploidy determination of squamous intraepithelial lesions in liquid-based cytologic samples (2002)

HPV typing and DNA measurements help in the objectivation of cytologic atypia and both can be performed efficiently from the same liquid-based cytologic samples.
Plasma Membrane Integrity and Survival of Melanoma Cells After Nanosecond Laser Pulses (2010)

Circulating tumor cells (CTCs) photoacoustic detection systems can aid clinical decision-making in the treatment of cancer. Interaction of melanin within melanoma cells with nanosecond laser pulses generates photoacoustic waves that make its detection possible. This study aims at: (1) determining melanoma cell survival after laser pulses of 6 ns at λ = 355 and 532 nm; (2) comparing the potential enhancement in the photoacoustic signal using λ = 355 nm in contrast with λ = 532 nm; (3) determining the critical laser fluence at which melanin begins to leak out from melanoma cells; and (4) developing a time-resolved imaging (TRI) system to study the intracellular interactions and their effect on the plasma membrane integrity. Monolayers of melanoma cells were grown on tissue culture-treated clusters and irradiated with up to 1.0 J/cm². Surviving cells were stained with trypan blue and counted using a hemacytometer. The phosphate buffered saline absorbance was measured with a nanodrop spectrophotometer to detect melanin leakage from the melanoma cells post-laser irradiation. Photoacoustic signal magnitude was studied at both wavelengths using piezoelectric sensors. TRI with 6 ns resolution was used to image plasma membrane damage. Cell survival decreased proportionally with increasing laser fluence for both wavelengths, although the decrease is more pronounced for 355 nm radiation than for 532 nm. It was found that melanin leaks from cells equally for both wavelengths. No significant difference in photoacoustic signal was found between wavelengths. TRI showed clear damage to plasma membrane due to laser-induced bubble formation.
Geodesic Polyarenes by Flash Vacuum Pyrolysis (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
The complete amino acid sequence of the Clostridium botulinum type‐E neurotoxin, derived by nucleotide‐sequence analysis of the encoding gene (1992)

The entire structural gene of the Clostridium botulinum NCTC 11219 type-E neurotoxin (BoNT/E) has been cloned as five overlapping DNA fragments, generated by polymerase chain reaction (PCR). Analysis of triplicate clones of each fragment, derived from three independent PCR, has allowed the derivation of the entire nucleotide sequence of the BoNT/E gene. Translation of the sequence has shown BoNT/E to consist of 1252 amino acids and, as such, represents the smallest BoNT characterised to date. The light chain of the toxin exhibits the highest level of sequence similarity to tetanus toxin (TeTx, 40%). The light chains of BoNT/A and BoNT/D share 33% similarity with BoNT/E, while BoNT/C exhibits 32% similarity. In contrast, the TeTx heavy chain exhibits the lowest degree of similarity (35%) with BoNT/E, with the BoNT heavy chains sharing 46%, 36% and 37%, for neurotoxin types A, C and D, respectively. Comparisons with partial amino acid sequences of the light chain of BoNT/E from C. botulinum strain Beluga and that from the strains Mashike, Iwanai and Otaru, indicate single amino acid differences in each case. Alignment of all characterised neurotoxin sequences (BoNT/A, BoNT/C, BoNT/D, BoNT/E and TeTx) shows them to be composed of highly conserved amino acid domains interspersed with amino acid tracts exhibiting little overall similarity. The most divergent region corresponds to the extreme COOH-terminus of each toxin, which may reflect differences in specificity of binding to neurone acceptor sites.
ABC of arterial and vascular disease: Vasculitis (2000)

Vasculitis is inflammation of blood vessel walls. The clinical and pathological features are variable and depend on the site and type of blood vessels that are affected. Diseases in which vasculitis is a primary process are called primary systemic vasculitides. 


The main types of vasculitides can be described using clinical features and pathological findings according to the Chapel Hill Consensus Conference. These names and definitions will be followed in this article. Definitive classification of systemic vasculitis is unsatisfactory since aetiology and pathogenesis are rarely known, and clinical and histological features overlap. Vasculitis may also occur as a secondary feature in other diseases, such as systemic lupus erythematosus and rheumatoid arthritis. 


Definitions of large vessel vasculitis
Giant cell arteritis (temporal arteritis)


Granulomatous arteritis of aorta and its major branches, especially extracranial branches of carotid artery


Often affects temporal artery


Usually occurs in patients older than 50 years


Often associated with polymyalgia rheumatica





Takayasu's arteritis


Granulomatous inflammation of aorta and its major branches


Usually occurs in patients younger than 50 years








Fever, night sweats, malaise, myalgia, and arthralgia are common in all types of vasculitis. Active vasculitis is usually associated with an acute phase response with an increase in C reactive protein concentration, erythrocyte sedimentation rate, or plasma viscosity.
The amphipathic α‐helix concept (1994)

An original series of 12- to 22-residue-long peptides was developed, they are only constituted by apolar Leu and charged Lys residues periodically located in the sequence in order to general ideal highly amphipathic alpha-helices. By circular dichroism, the peptides are proven to be mainly alpha-helical in organic and aqueous solvents and in the presence of lipids. The peptides are highly hemolytic, their activity varies according to the peptide length. The 15-, 20-, and 22-residue-long-peptides have LD50 approximately 5 x 10(-8) M for 10(7) erythrocytes, i.e. they are 5-10 times more active than melittin, and are indeed several orders of magnitude more active than magainin or mastoparan.
Fabrication of Lithographically Defined Chemically Patterned Polymer Brushes and Mats (2011)

Chemically patterned surfaces comprised of polymer mats and brushes of well-defined chemistry were fabricated at the length scale of 10 nm. A key concept is the integration of new materials, cross-linked polymer mats, with traditional lithographic processing. Resist was patterned on top of cross-linked polystyrene mats. After etching, regions of the remaining mat with dimensions ranging from 10 to 35 nm were separated by interspatial openings to the underlying substrate. End-grafted polymer brushes, in this case hydroxyl-terminated poly(2-vinylpyridine) or polystyrene−poly(methyl methacrylate) random copolymer, were grafted into the exposed, interspatial regions from films spin-coated over the patterned mat. Both block copolymer wetting studies, with polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA), and near-edge X-ray fine structure spectroscopy showed that with sufficient cross-linking the polymer mat chemistry was unaffected by the subsequent grafting of the polymer brush. The precise definition of both the chemistry and the geometry was demostrated with two sensitive applications of nanoscale chemical patterns: the site-specific immobilization of Au nanoparticles and the directed assembly of overlying PS-b-PMMA films.
Identification of negative and positive regulatory elements in the human renin gene (1989)

Renin gene expression is tissue-specific and under complex hormonal control. To investigate which DNA elements are involved in the control of human renin gene expression, we performed transient DNA transfer experiments with renin-chloramphenicol acetyltransferase fusions. We have mapped a complex arrangement of positive and negative control sequences in the 5' flanking region of the human renin gene. One positive control element is active in either orientation and defines a renin gene enhancer. The negative element is also active in either orientation and defines a renin gene silencer. Mapping in the same region as the silencer is a cAMP-responsive element, a sequence conserved in mouse, rat, and human renin genes.
Suppression of Human Glioma Xenografts with Second-Generation IL13R-Specific Chimeric Antigen Receptor–Modified T Cells (2012)

These data raise the possibility of immune targeting of diffusely invasive GBM cells either via dTc infusion into resection cavities to prevent GBM recurrence or via direct stereotactic injection of dTcs to suppress inoperable or recurrent tumors. Systemic administration of these IL13 dTc could be complicated by reaction against normal tissues expressing IL13Ra1.
Reversal of visuospatial hemi-inattention in patients with chronic progressive multiple sclerosis by treatment with weak electromagnetic fields (1994)

The occurrence of cognitive impairment including visuoperceptive and visuospatial deficits have long been recognized to occur in patients with multiple sclerosis (MS) particularly among patients with a chronic progressive course. In MS visuospatial and visuoperceptive deficits have been attributed to the presence of diffuse demyelinating plaques which "disconnect" the brainstem reticular formation and other subcortical structures involved in attention and arousal from cortical areas thus causing a state of hypoarousal. It has been reported recently that brief external applications of alternating pulsed electromagnetic fields (EMFs) in the picotesla (pT) range intensity improved visuoperceptive and visuospatial functions in MS patients. The present communication concerns three female patients with chronic progressive course of MS (mean age: 52.3 +/- 2.0 yrs; mean duration of illness: 17.6 +/- 10.2 yrs) who, on tests of free drawings, demonstrated visuospatial hemi-inattention as a feature of more global cognitive deterioration. In all patients brief applications of EMFs rapidly reversed this cognitive deficit. These findings support prior observations demonstrating that pT EMFs may bring about reversal of certain cognitive deficits in MS patients which, to my knowledge, remain unaffected by any other treatment modality.
Gene encoding the major subunit of CS1 pili of human enterotoxigenic Escherichia coli (1990)

Some enterotoxigenic strains of Escherichia coli (ETEC) utilize the CS1 pilus for colonization of human intestinal epithelium. We have cloned the gene which encodes the major CS1 subunit and called it cooA (for coli surface antigen one). Hybridization showed that the ETEC strain from which it was cloned carried cooA on a plasmid different from the one encoding its positive regulator, rns. Based on the cooA DNA sequence, cleavage with signal peptidase would be expected to produce a mature protein of 15.2 kDa; a 16-kDa polypeptide that reacted with CS1-specific antiserum was observed on electrophoresis. At the protein level, there was 92% similarity and 55% identity between cooA and cfaB, the major colonization factor antigen I (CFA/I) antigen. However, CS1-specific antisera did not react with CfaB. No hybridization was seen between either of two different cooA probes and total DNA from ETEC strains expressing AFA-1, CFA/I, CS2, CS3, CS4, CS5, or CS6.
Hepatocellular carcinoma (2015)

Hepatocellular carcinoma (HCC), one of the serious complications of cirrhosis, is the second leading cause of cancer-related deaths in males worldwide. Besides prevention of HCC development by hepatitis B virus vaccination in endemic regions, early detection is the only effective measure to increase survival and to decrease public health burden. Although HCC is an appropriate type of cancer for conducting surveillance program, the current strategy to detect HCC at early stage using ultrasound and serologic markers is not optimal. Clinical diagnosis of HCC largely depends on the characteristics of hypervascular cancer, and has evolved due to the improvement of imaging techniques including computed tomography scan and magnetic resonance imaging. Staging systems suggested so far have tried to integrate tumor extent, liver function, and patient's performance status to link an available treatment method and predict survival. Further exploration for improved treatement in advanced stage and molecular classification is necessary. Resection and local ablation can achieve cure in small (≤2 cm) HCC, and liver transplantation is effective in that HCC-prone liver is also replaced. Transarterial chemoembolization (TACE) is the most commonly used therapy for multiple HCC, and was found to increase patient survival. New catheter-based treatments such as DC Bead TACE and Yttrium-90 radioembolization have been developed and await long-term results. As an alternative, external beam radiation therapy has s a potent antitumor effect with minimal adverse effect. With the advent of sorafenib, the era of molecular targeted therapy for HCC has begun. In spite of improvement of each treatment modality, a multidisciplinary team approach is mandatory for the optimal HCC management due to the heterogeneity of the cancer and high rate of recurrence. MicroRNA (miR) technology including anti-microRNA (antagomir) and miR-mimetics could be an emerging field of HCC treatment.
Three-dimensional forward solver and its performance analysis for magnetic resonance electrical impedance tomography (MREIT) using recessed electrodes (2003)

In magnetic resonance electrical impedance tomography (MREIT), we try to reconstruct a cross-sectional resistivity (or conductivity) image of a subject. When we inject a current through surface electrodes, it generates a magnetic field. Using a magnetic resonance imaging (MRI) scanner, we can obtain the induced magnetic flux density from MR phase images of the subject. We use recessed electrodes to avoid undesirable artefacts near electrodes in measuring magnetic flux densities. An MREIT image reconstruction algorithm produces cross-sectional resistivity images utilizing the measured internal magnetic flux density in addition to boundary voltage data. In order to develop such an image reconstruction algorithm, we need a three-dimensional forward solver. Given injection currents as boundary conditions, the forward solver described in this paper computes voltage and current density distributions using the finite element method (FEM). Then, it calculates the magnetic flux density within the subject using the Biot-Savart law and FEM. The performance of the forward solver is analysed and found to be enough for use in MREIT for resistivity image reconstructions and also experimental designs and validations. The forward solver may find other applications where one needs to compute voltage, current density and magnetic flux density distributions all within a volume conductor.
Generating mouse models for biomedical research: technological advances (2019)

Over the past decade, new methods and procedures have been developed to generate genetically engineered mouse models of human disease. This At a Glance article highlights several recent technical advances in mouse genome manipulation that have transformed our ability to manipulate and study gene expression in the mouse. We discuss how conventional gene targeting by homologous recombination in embryonic stem cells has given way to more refined methods that enable allele-specific manipulation in zygotes. We also highlight advances in the use of programmable endonucleases that have greatly increased the feasibility and ease of editing the mouse genome. Together, these and other technologies provide researchers with the molecular tools to functionally annotate the mouse genome with greater fidelity and specificity, as well as to generate new mouse models using faster, simpler and less costly techniques.
Synthesis, Crystallization, and Biological Evaluation of an Orally Active Prodrug of Gemcitabine (2009)

The design, synthesis, and biological characterization of an orally active prodrug (3) of gemcitabine are described. Additionally, the identification of a novel co-crystal solid form of the compound is presented. Valproate amide 3 is orally bioavailable and releases gemcitabine into the systemic circulation after passing through the intestinal mucosa. The compound has entered clinical trials and is being evaluated as a potential new anticancer agent.