gebhart/patrepeval huggingface dataset:
Nerve fiber growth in culture on fibronectin, collagen, and glycosaminoglycan substrates (1983)

In an initial report (Carbonetto, S. T., M. M. Gruver, and D. C. Turner (1982) Science 216: 897-899) we described the use of 2-hydroxyethylmethacrylate (HEMA) in preparing defined culture substrates for studying nerve fiber growth. In those studies fibronectin and collagen were conspicuous, among a variety of HEMA-embedded proteins, in supporting fiber growth of embryonic neurons from chick dorsal root ganglia. Here we further document and extend our preliminary studies, especially with regard to the interaction of growing nerve fibers with fibronectin. HEMA substrates were prepared with proteolytic fragments of fibronectin, each of which had one or more of the functional sites of the intact molecule. Only those fragments of fibronectin that retained the region of the molecule known to mediate myoblast attachment were active in supporting nerve fiber growth. When added in excess to the culture medium, the smallest of the active fragments inhibited fiber growth on substrates that contained intact fibronectin. In culture medium depleted of serum fibronectin, HEMA gels containing collagens purified from connective tissues (types I and III) or from basement membranes (type IV) were about as effective as HEMA substrates containing fibronectin in supporting fiber growth. Nerve fiber growth on collagen substrates proceeded in the absence of fibronectin in the culture medium. Several glycosaminoglycans (heparin, chondroitin sulfate, hyaluronic acid) were ineffective as substrates for fiber growth. Treatment of HEMA/ fibronectin gels with heparin or incorporation of heparin along with fibronectin in the gel profoundly diminished the efficacy of fibronectin in supporting nerve fiber growth. Our studies suggest that the growth of nerve fibers on fibronectin substrates results from direct interaction with a specific portion of the fibronectin molecule and that this interaction can be inhibited by heparin and possibly other glycosaminoglycans.
Choosing the right sugar: How polymerases select a nucleotide substrate (1997)

A quick glance at the recent scientific literature might give the impression that nucleic acid polymerases are suffering from an identity crisis. The last few years have brought us “E. coli DNA polymerase I as a reverse transcriptase” (1), “A mutant T7 RNA polymerase as a DNA polymerase” (2), and, in a recent issue of the Proceedings, “Conferring RNA polymerase activity to a DNA polymerase: A single residue in reverse transcriptase controls substrate selection” (3).
Blood, sweat, and tears: developing clinically relevant protein biosensors for integrated body fluid analysis (2015)

Biosensors are being developed to provide rapid, quantitative, diagnostic information to clinicians in order to help guide patient treatment, without the need for centralised laboratory assays. The success of glucose monitoring is a key example of where technology innovation has met a clinical need at multiple levels – from the pathology laboratory all the way to the patient's home. However, few other biosensor devices are currently in routine use. Here we review the challenges and opportunities regarding the integration of biosensor techniques into body fluid sampling approaches, with emphasis on the point-of-care setting.
Superconducting low-inductance undulatory galvanometer microwave amplifier (2012)

We describe a microwave amplifier based on the superconducting low-inductance undulatory galvanometer (SLUG). The SLUG is embedded in a microstrip resonator, and the signal current is injected directly into the device loop. Measurements at 30 mK show gains of 25 dB at 3 GHz and 15 dB at 9 GHz. Amplifier performance is well described by a simple numerical model based on the Josephson junction phase dynamics. We expect optimized devices based on high critical current junctions to achieve gain greater than 15 dB, bandwidth of several hundred MHz, and added noise of order one quantum in the frequency range of 5-10 GHz.
The elucidation of novel capsular genotypes of Haemophilus influenzae type b with the polymerase chain reaction (1995)

Molecular characterization is an important pre-requisite for post-vaccine studies of Haemophilus influenzae type b (Hib). Three capsular genotyping patterns, b(S), b(G) and b(V), have been described in the major phylogenetic lineage of Hib. However, in a recent series of prospective studies, three new hybridisation patterns were observed among 425 strains of Hib. Four pairs of polymerase chain reaction (PCR) primers were used to identify the capsular gene (cap) structure of these Hib strains. This showed that the strains possessed simple DNA re-arrangements. In two instances a change in restriction enzyme recognition site was the most likely cause of the new hybridisation pattern. The third strain possessed a cap b locus consisting of intact tandem repeats of cap b in a b(S) background. It was reasoned that a similar cap b locus would not be readily recognised by hybridisation in a b(G) background, and b(G) strains were therefore characterized by the PCR method. This showed one of 35 b(G) strains to possess a cap locus with intact tandem repeat copies of cap b. The novel capsular genotypes described here are rare, but can be detected rapidly and accurately by a combination of PCR and capsular genotyping hybridisation patterns.
Classifying Gene Expression Profiles from Pairwise mRNA Comparisons (2004)

We present a new approach to molecular classification based on mRNA comparisons. Our method, referred to as the top-scoring pair(s) (TSP) classifier, is motivated by current technical and practical limitations in using gene expression microarray data for class prediction, for example to detect disease, identify tumors or predict treatment response. Accurate statistical inference from such data is difficult due to the small number of observations, typically tens, relative to the large number of genes, typically thousands. Moreover, conventional methods from machine learning lead to decisions which are usually very difficult to interpret in simple or biologically meaningful terms. In contrast, the TSP classifier provides decision rules which i) involve very few genes and only relative expression values (e.g., comparing the mRNA counts within a single pair of genes); ii) are both accurate and transparent; and iii) provide specific hypotheses for follow-up studies. In particular, the TSP classifier achieves prediction rates with standard cancer data that are as high as those of previous studies which use considerably more genes and complex procedures. Finally, the TSP classifier is parameter-free, thus avoiding the type of over-fitting and inflated estimates of performance that result when all aspects of learning a predictor are not properly cross-validated.
Pathways for the incorporation of exogenous fatty acids into phosphatidylethanolamine in Escherichia coli. (1985)

Two distinct pathways for the incorporation of exogenous fatty acids into phospholipids were identified in Escherichia coli. The predominant route originates with the activation of fatty acids by acyl-CoA synthetase followed by the distribution of the acyl moieties into all phospholipid classes via the sn-glycerol-3-phosphate acyltransferase reaction. This pathway was blocked in mutants (fadD) lacking acyl-CoA synthetase activity. In fadD strains, exogenous fatty acids were introduced exclusively into the 1-position of phosphatidylethanolamine. This secondary route is related to 1-position fatty acid turnover in phosphatidylethanolamine and proceeds via the acyl-acyl carrier protein synthetase/2-acylglycerophosphoethanolamine acyltransferase system. The turnover pathway exhibited a preference for saturated fatty acids, whereas the acyl-CoA synthetase-dependent pathway was less discriminating. Both pathways were inhibited in mutants (fadL) lacking the fatty acid permease, demonstrating that the fadL gene product translocates exogenous fatty acids to an intracellular pool accessible to both synthetases. These data demonstrate that acyl-CoA synthetase is not required for fatty acid transport in E. coli and that the metabolism of exogenous fatty acids is segregated from the metabolism of acyl-acyl carrier proteins derived from fatty acid biosynthesis.
ConcertTalk: A Weekend With a Portable Audio Space (1997)

This paper describes a study of the ConcertTalk system, a portable audio space that was used for two days. Two-way radios were provided to attendees at Lollapalooza rock concerts, and their use was recorded and analyzed. The study’s participants quickly began using the system, used it throughout the day, and found many creative ways for the radios to improve the Lollapalooza concert experience. ConcertTalk’s results suggest the utility of studying CHI technologies outside of work places, both to validate and expand the foundational theory of our growing domain of knowledge in practice.
Prognostic implications of YKL-40 overexpression in breast cancer (2006)

20115 Background: YKL-40 has been implicated as a connective tissue growth factor and a migratory factor for endothelial cells. Elevated serum levels of YKL-40 have been found to correlate with worse survival in a variety of malignancies including breast cancer. We wished to determine if tumor overexpression of this protein also had prognostic implications in breast cancer. Methods: A prospectively collected database of breast cancer patients treated at the University Hospital of Newark was used for analysis. Immunohistochemical analysis was performed on 115 patients for whom full clinical information and follow up was available. Specimens were categorized as lacking immunoreactivity (0), having focal sparse immunoreactivity (1), or strong more diffuse immunoreactivity (2). Results: YKL-40 expression was noted in 38 patients (33%). Of these, 24 demonstrated strong (2) immunoreactivity (21%). Strong (2) YKL-40 immunoreactivity significantly correlated with larger tumor size (p &lt; .05). Tumors expressing any level of YKL-40 were also significantly more likely to be estrogen and/or progesterone receptor negative (p &lt; .01). No significant correlation was demonstrated between YKL-40 status and nodal stage. At a mean follow up of 2.3 years, disease-free survival was significantly worse in the subset of patients whose tumors overexpressed any level of YKL-40 compared to the non-expressors (p &lt; .01). In multivariate analysis, YKL-40 status was independent of T-stage and N-stage in predicting disease recurrence. Conclusions: Immunoreactivity for YKL-40 was a significant predictor of breast cancer relapse in this subset of patients. This was independent of T or N-stage and suggests that tumor immunohistochemistry for this protein may be a valuable prognostic marker in breast cancer. No significant financial relationships to disclose.
New Anticoagulant Therapy (2004)

The development of new anticoagulants is expanding the list of drugs that can be used to prevent and treat venous and arterial thrombosis. New parenteral anticoagulants have been developed to overcome the limitations of heparin and low-molecular-weight heparin, whereas novel orally active anticoagulants have been designed to provide more streamlined therapy than vitamin K antagonists. This review identifies the molecular targets of new anticoagulants, describes the results of clinical trials, and provides clinical perspective on the opportunities for new anticoagulants.
Asialoglycoprotein receptor function in benign liver disease: evaluation with MR imaging. (1991)

An arabinogalactan-coated ultrasmall superparamagnetic iron oxide (AG-USPIO) preparation specific for asialoglycoprotein (ASG) receptors on hepatocytes was used as a magnetic resonance (MR) imaging contrast agent in the evaluation of a spectrum of benign liver diseases in animal models. The activity of hepatocyte ASG receptors, which directly reflects liver function, was directly assessed by measuring liver relaxation times in vitro and MR signal intensity in vivo. The following measurements allowed three-dimensional assessment of liver function: (a) liver relaxation time, (b) native MR signal intensities of liver, (c) response of liver to the AG-USPIO probe (percentage decrease of liver signal intensity after intravenous administration of 10 mumol/kg of AG-USPIO: normal liver 55%, fatty liver 57%, acute hepatitis 36%, chronic hepatitis 29%, and cirrhosis 46%), and (d) redistribution of hepatocyte-specific AG-USPIO to the spleen (present in hepatitis and cirrhosis but not in normal liver and fatty liver). The results of this study indicate that cellular hepatic abnormalities can be detected and quantitated with MR receptor imaging.
Tumor Antigens Recognized by T Lymphocytes (1994)

Transplantation experiments have demonstrated that most mouse tumors express antigens that can constitute targets for rejection responses mediated by syngeneic T lymphocytes. For human tumors, autologous cultures mixing tumor cells and blood lymphocytes or tumor-infiltrating lymphocytes have produced CD8+ and CD4+ cytolytic T cell (CTL) clones that recognize tumor cells specifically. Attempts to identify the target antigens by biochemical fractionation of tumor cells up to now have failed, with the important exception of the identification of underglycosylated mucins present on breast and pancreatic carcinomas. Gene transfection approaches have proved more successful. A gene family named MAGE codes for antigens recognized by autologous CTL on a melanoma tumor. These genes are not expressed in normal tissues except for testis. They are expressed in many tumors of several histological types. Differentiation antigens coded by genes such as tyrosinase are also recognized on human melanoma by autologous CTL. The identification of human tumor rejection antigens opens new possibilities for systematic approaches to the specific immune therapy of cancer.
Structural and transcriptional analysis of human papillomavirus type 16 sequences in cervical carcinoma cell lines (1987)

We cloned and analyzed the integrated human papillomavirus type 16 (HPV-16) genomes that are present in the human cervical carcinoma cell lines SiHa and CaSki. The single HPV-16 genome in the SiHa line was cloned as a 10-kilobase (kb) HindIII fragment. Integration of the HPV-16 genome occurred at bases 3132 and 3384 with disruption of the E2 and E4 open reading frames (ORFs). An additional 52-base-pair deletion of HPV-16 sequences fused the E2 and E4 ORFs. the 5' portion of the disrupted E2 ORF terminated immediately in the contiguous human right-flanking sequences. Heteroduplex analysis of this cloned integrated viral genome with the prototype HPV-16 DNA revealed no other deletions, insertions, or rearrangements. DNA sequence analysis of the E1 ORF, however, revealed the presence of an additional guanine at nucleotide 1138, resulting in the fusion of the E1a and E1b ORFs into a single E1 ORF. Sequence analysis of the human flanking sequences revealed one-half of an Alu sequence at the left junction and a sequence highly homologous to the human O repeat in the right-flanking region. Analysis of the three most abundant BamHI clones from the CaSki line showed that these consisted of full-length, 7.9-kb HPV-16 DNA; a 6.5-kb genome resulting from a 1.4-kb deletion of the long control region; and a 10.5-kb clone generated by a 2.6-kb tandem repeat of the 3' early region. These HPV-16 genomes were arranged in the host chromosomes as head-to-tail, tandemly repeated arrays. Transcription analysis revealed expression of the HPV-16 genome in each of these two cervical carcinoma cell lines, albeit at significantly different levels. Preliminary mapping of the viral RNA with subgenomic strand-specific probes indicated that viral transcription appeared to be derived primarily from the E6 and E7 ORFs.
Comparison of Intracardiac Cell Transplantation: Autologous Skeletal Myoblasts Versus Bone Marrow Cells (2003)

Transplantation and myogenic differentiation of bone marrow-derived progenitor cells increased regional systolic heart function after myocardial injury to a similar degree as skeletal myoblasts.
The Relationship Between Severity of Illness and Hospital Length of Stay and Mortality (1991)

To address the question of quantification of severity of illness on a wide scale, the Computerized Severity Index (CSI) was developed by a research team at the Johns Hopkins University. This article describes an initial assessment of some aspects of the validity and reliability of the CSI on a sample of 2,378 patients within 27 high-volume DRGs from five teaching hospitals. The 27 DRGs predicted 27% of the variation in LOS, while DRGs adjusted for Admission CSI scores predicted 38% and DRGs adjusted for Maximum CSI scores throughout the hospital stay predicted 54% of this variation. Thus, the Maximum CSI score increased the predictability of DRGs by 100%. We explored the impact of including a 7-day cutoff criterion along with the Maximum CSI score similar to a criterion used in an alternative severity of illness measure. The DRG/Maximum CSI score's predictive power increased to 63% when the 7-day cutoff was added to the CSI definition. The Admission CSI score was used to predict in-hospital mortality and correlated R = 0.603 with mortality. The reliability of Admission and Maximum CSI data collection was high, with agreement of 95% and kappa statistics of 0.88 and 0.90, respectively.
Toward [18F]-Labeled Aryltrifluoroborate Radiotracers: In Vivo Positron Emission Tomography Imaging of Stable Aryltrifluoroborate Clearance in Mice (2008)

The use of a boronic ester as a captor of aqueous [(18)F]-fluoride has been previously suggested as a means of labeling biomolecules in one step for positron emission tomography (PET) imaging. For this approach to be seriously considered, the [(18)F]-labeled trifluoroborate should be humorally stable such that it neither leaches free [(18)F]-fluoride to the bone nor accumulates therein. Herein, we have synthesized a biotinylated boronic ester that is converted to the corresponding trifluoroborate salt in the presence of aqueous [(18)F]-fluoride. In keeping with its in vitro aqueous kinetic stability at pH 7.5, the trifluoroborate appears to clear in vivo quite rapidly to the bladder as the stable trifluoroborate salt with no detectable leaching of free [(18)F]-fluoride to the bone. When this labeled biotin is preincubated with avidin, the pharmacokinetic clearance of the resulting complex is visibly altered. This work validates initial claims that boronic esters are potentially useful as readily labeled precursors to [(18)F]-PET reagents.
On the right path. Collaborative case management makes nurses partners in the care-planning process. (1993)

The quality improvement movement in healthcare has given nurses a greater role in developing and implementing collaborative case management processes. In the case management model, nurses no longer simply take orders but actively participate in designing a plan of care. At Mercy Health Center, Oklahoma City, nurses play a leading role in the development of "clinical pathways," plans of care for a single diagnosis as directed by a specific physician or group of physicians. The pathways promote multidisciplinary, interdepartmental cooperation in patient care. Since August 1992, Mercy has developed clinical pathways for five inpatient and outpatient procedures, and more are being considered. Once a plan has been created, its key points are rewritten in lay terms and printed in a brochure for the patient. During the treatment, nurses and other healthcare professionals document when specific steps in the plan have been completed. In follow-up evaluations Mercy's steering committee for the collaborative care process has found that the clinical pathways have maximized quality, improved efficiency, increased patient satisfaction, and enhanced collaborative team practice.
Hydrocarbons (2000)

Abstract The article contains sections titled: 1. Saturated Hydrocarbons 1.1. Physical Properties 1.2. Chemical Properties 1.3. Production 1.3.1. From Natural Gas and Petroleum 1.3.2. From Coal and Coal‐Derived Products 1.3.3. By Synthesis and by Conversion of other Hydrocarbons 1.4. Uses 1.5. Individual Saturated Hydrocarbons 2. Olefins 2.1. Monoolefins 2.1.1. Properties 2.1.2. Production of Higher Olefins 2.1.2.1. Production from Paraffins 2.1.2.2. Oligomerization of Lower Olefins 2.1.3. Uses of Higher Olefins 2.1.4. Economic Aspects of Higher Olefins 2.2. Dienes and Polyenes 2.2.1. Low Molecular Mass 1,3‐Dienes 2.2.2. Synthesis of Dienes and Polyenes by Oligomerization 2.2.3. Synthesis of Dienes and Polyenes by Metathesis 3. Alkylbenzenes 3.1. Trimethylbenzenes 3.2. Tetramethylbenzenes 3.3. Penta‐ and Hexamethylbenzene 3.4. Diethylbenzenes 3.5. Triethylbenzenes and more highly Ethylated Benzenes 3.6. Ethylmethylbenzenes (Ethyltoluenes) 3.7. Cumene 3.8. Diisopropylbenzenes 3.9. Cymenes; C 4 ‐ and C 5 ‐Alkylaromatic Compounds 3.10. Monoalkylbenzenes with Alkyl Groups &gt;C 10 3.11. Diphenylmethane 4. Biphenyls and Polyphenyls 4.1. Biphenyl 4.2. Terphenyls 4.3. Polyphenyls 5. Hydrocarbons from Coal Tar 5.1. Acenaphthene 5.2. Indene 5.3. Fluorene 5.4. Fluoranthene 5.5. Phenanthrene 5.6. Pyrene 6. Toxicology and Occupational Health 6.1. Alkanes 6.2. Alkenes 6.3. Alkylbenzenes 6.4. Biphenyls and Polyphenyls 6.5. Hydrocarbons from Coal Tar 6.5.1. Biological Effects 6.5.1.1. Carcinogenicity and Mutagenicity 6.5.1.2. Mammalian Toxicity and Toxicokinetics 6.5.1.3. Ecotoxicology 6.5.2. Safety Regulations
Multispectral image compression algorithms (2002)

This paper presents a data compression algorithm capable of significantly reducing the amounts of information contained in multispectral and hyperspectral images. The loss of information ranges from a perceptually lossless level, achieved at 20-30:1 compression ratios, to a one where exploitation of the images is still possible (over 100:1 ratios). A one-dimensional transform coder removes the spectral redundancy, and a two-dimensional wavelet transform removes the spatial redundancy of multispectral images. The transformed images are subsequently divided into active regions that contain significant wavelet coefficients. Each active block is then hierarchically encoded using multidimensional bitmap trees. Application of reversible histogram equalization methods on the spectral bands can significantly increase the compression/distortion performance. Landsat Thematic Mapper data are used to illustrate the performance of the proposed algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>