gebhart/patrepeval huggingface dataset:
Rapid, high throughput prenatal detection of aneuploidy using a novel quantitative method (MLPA) (2003)

Prenatal diagnosis of syndromes caused by chromosomal abnormality is a long established part of obstetric care in developed countries. In this area, there have been recent significant advances in the identification of high risk pregnancies using sophisticated serum analyte and ultrasound screening methods.1,2 For follow up diagnostic testing, karyotyping has provided the gold standard. This technology has remained essentially unchanged over 30 years, as no new technology has yet proven superior in terms of being able to detect such a wide range of abnormalities with the necessary precision. Nevertheless, molecular tests, such as fluorescent in situ hybridisation (FISH) 3 and short tandem repeat analysis,4 are now in common practice for the diagnosis of specific abnormalities. These adjunctive tests importantly decrease turnaround times from 1–2 weeks to 1–2 days.

We assessed the performance of multiplex ligation dependent probe amplification (MLPA) as an alternative method for the detection of aneuploidy, which is by far the most common prenatal chromosome abnormality. This novel technique5 detects sequence dosage differences in a semi-quantitative manner and has many potential applications in diagnostic molecular genetics and cytogenetics. For example, a recent report describes its use for detection of large genomic deletions and duplications in the BRCA1 gene.6 This technology appears to have significant advantages in that it is extremely versatile in its applications, flexible in its target loci, highly automated, suitable for high throughput testing, efficient, and cost effective. Its application for aneuploidy detection has not been reported in a clinical setting. In order to assess the precision and robustness of the test, we conducted a prospective blind trial on 492 consecutive amniocentesis samples referred to our cytogenetics laboratory.

### Study design

This study was designed to blind test amniocentesis samples prospectively. The samples were collected over a 4 month period as they were referred …
In vitro stimulation of articular chondrocyte mRNA and extracellular matrix synthesis by hydrostatic pressure (1996)

This study tested the effects of hydrostatic pressure (10 MPa) on adult articular chondrocyte mRNA and extracellular matrix synthesis in vitro. High density primary cultures of bovine chondrocytes were exposed to hydrostatic pressure applied intermittently at 1 Hz or constantly for 4 hours in serum-free medium or in medium containing 1% fetal bovine serum. mRNAs for aggrecan, types I and II collagen, and beta-actin were analyzed by Northern blots and quantified by slot blots. Proteoglycan synthesis was quantified by 35SO4 uptake into cetylpyridinium chloride-precipitable glycosaminoglycans, and cell-associated aggrecan and type-II collagen were detected by immunohistochemical techniques. In serum-free medium, intermittent pressure increased aggrecan mRNA signal by 14% and constant pressure decreased type-II collagen mRNA signal by 16% (p < 0.05). In the presence of 1% fetal bovine serum, intermittent pressure increased aggrecan and type-II collagen mRNA signals by 31% (p < 0.01) and 36% (p < 0.001), respectively, whereas constant pressure had no effect on either mRNA. Intermittent and constant pressure stimulated glycosaminoglycan synthesis 65% (p < 0.001) and 32% (p < 0.05), respectively. Immunohistochemical detection of cell-associated aggrecan and type-II collagen was increased in response to both intermittent and constant pressure. These data support the hypothesis that physiologic hydrostatic pressure directly influences the extracellular matrix metabolism of articular chondrocytes.
Mutational Effects On Protein Stability (1989)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Classical Conditioning and Brain Systems: The Role of Awareness (1998)

Classical conditioning of the eye-blink response, perhaps the best studied example of associative learning in vertebrates, is relatively automatic and reflexive, and with the standard procedure (simple delay conditioning), it is intact in animals with hippocampal lesions. In delay conditioning, a tone [the conditioned stimulus (CS)] is presented just before an air puff to the eye [the unconditioned stimulus (US)]. The US is then presented, and the two stimuli coterminate. In trace conditioning, a variant of the standard paradigm, a short interval (500 to 1000 ms) is interposed between the offset of the CS and the onset of the US. Animals with hippocampal lesions fail to acquire trace conditioning. Amnesic patients with damage to the hippocampal formation and normal volunteers were tested on two versions of delay conditioning and two versions of trace conditioning and then assessed for the extent to which they became aware of the temporal relationship between the CS and the US. Amnesic patients acquired delay conditioning at a normal rate but failed to acquire trace conditioning. For normal volunteers, awareness was unrelated to successful delay conditioning but was a prerequisite for successful trace conditioning. Trace conditioning is hippocampus dependent because, as in other tasks of declarative memory, conscious knowledge must be acquired across the training session. Trace conditioning may provide a means for studying awareness in nonhuman animals, in the context of current ideas about multiple memory systems and the function of the hippocampus.
Small animal model species are not created equal (2012)

Heart Research Laboratory, Department of Physiology and Pharmacology, School of Biomedical Sciences, James Cook University, Queensland, Australia
Systems Study for an Integrated Digital/Electric Aircraft (IDEA). (1985)

The results of the Integrated Digital/Electric Aircraft (IDEA) Study are presented. Airplanes with advanced systems were, defined and evaluated, as a means of identifying potential high payoff research tasks. A baseline airplane was defined for comparison, typical of a 1990's airplane with advanced active controls, propulsion, aerodynamics, and structures technology. Trade studies led to definition of an IDEA airplane, with extensive digital systems and electric secondary power distribution. This airplane showed an improvement of 3% in fuel use and 1.8% in DOC relative to the baseline configuration. An alternate configuration, an advanced technology turboprop, was also evaluated, with greater improvement supported by digital electric systems. Recommended research programs were defined for high risk, high payoff areas appropriate for implementation under NASA leadership.
Variants in Nicotinic Receptors and Risk for Nicotine Dependence (2008)

This study confirms that at least two independent variants in this nicotinic receptor gene cluster contribute to the development of habitual smoking in some populations, and it underscores the importance of multiple genetic variants contributing to the development of common diseases in various populations.
Recombinant polypeptide from the endonuclease region of the acquired immune deficiency syndrome retrovirus polymerase (pol) gene detects serum antibodies in most infected individuals (1986)

Sera from the majority of individuals that were positive in an enzyme-linked immunosorbent assay (ELISA) retrovirus (ARV), an isolate of the for antibodies to acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV), an isolate of the retrovirus identified as the etiologic agent of AIDS, were found to react with a 31,000-dalton protein (p31) in virus Western blot assays. To determine if this 31,000-dalton immunoreactive species originated from the putative endonuclease region of the polymerase (pol) gene of ARV, we cloned this portion of pol into bacterial expression vectors for direct expression and for expression as a fusion protein with human superoxide dismutase. Transformants from both constructions expressed immunoreactive protein detected in immunoblots with an AIDS patient's serum. Extracts from transformants expressing these sequences competed with the binding of antibodies from AIDS patients' sera to the 31,000-dalton protein in virus immunoblots, confirming that viral p31 originated from the endonuclease domain of the ARV polymerase gene. The superoxide dismutase-p31 fusion protein was purified, and an ELISA for detecting antibodies to p31 was developed. The majority (95%) of serum samples obtained from individuals seropositive in the virus ELISA were also positive in the p31 antibody ELISA.
Six-locus high resolution HLA haplotype frequencies derived from mixed-resolution DNA typing for the entire US donor registry (2013)

We have calculated six-locus high resolution HLA A∼C∼B∼DRB3/4/5∼DRB1∼DQB1 haplotype frequencies using all Be The Match(®) Registry volunteer donors typed by DNA methods at recruitment. Mixed resolution HLA typing data was inputted to a modified expectation-maximization (EM) algorithm in the form of genotype lists generated by interpretation of primary genomic typing data to the IMGT/HLA v3.4.0 allele list. The full cohort consists of 6.59 million subjects categorized at a broad race level. Overall 25.8% of the individuals were typed at the C locus, and 5.2% typed at the DQB1 locus, while all individuals were typed for A, B, DRB1. We also present a subset of 2.90 million subjects with detailed race/ethnic information mapped to 21 population subgroups, 64.1% of which have primary DNA typing data across at least A, B, and DRB1 loci. Sample sizes at the detailed race level range from 1,242,890 for European Caucasian to 1,376 Alaskan Native or Aleut. Genetic distance measurements show high levels of HLA genetic divergence among the 21 detailed race categories, especially among the eight Asian-American populations. These haplotype frequencies will be used to improve match predictions for donor selection algorithms for hematopoietic stem cell transplantation and improve the accuracy in modeling registry match rates.
Diazo compounds for the bioreversible esterification of proteins (2014)

A diazo compound is shown to convert carboxylic acids to esters efficiently in an aqueous environment. The basicity of the diazo compound is critical: low basicity does not lead to a reaction but high basicity leads to hydrolysis. This reactivity extends to carboxylic acid groups in a protein. The ensuing esters are hydrolyzed by human cellular esterases to regenerate protein carboxyl groups. This new mode of chemical modification could enable the key advantages of prodrugs to be translated from small-molecules to proteins.
Preparation and Synthetic Utility of Some Organotin Derivatives of nucleosides (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and Synthetic Utility of Some Organotin Derivatives of nucleosidesDaniel Wagner, Julien P. H. Verheyden, and John G. MoffattCite this: J. Org. Chem. 1974, 39, 1, 24–30Publication Date (Print):January 1, 1974Publication History Published online1 May 2002Published inissue 1 January 1974https://pubs.acs.org/doi/10.1021/jo00915a005https://doi.org/10.1021/jo00915a005research-articleACS PublicationsRequest reuse permissionsArticle Views1547Altmetric-Citations259LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
<title>Monolithic integration in III-V semiconductors via a universal damage enhanced quantum well intermixing technique</title> (1998)

A novel technique for quantum well intermixing is demonstrated which has proven to be a reliable means for obtaining post-growth shifts in the band edge of a wide range of III-V material systems. The techniques relies upon the generation of point defects via plasma induced damage during the deposition of sputtered silica, and provides a simple and reliable process for the fabrication of both wavelength tuned lasers and monolithically integrated devices. Wavelength tuned board area oxide stripe lasers are demonstrated in InGaAs-InAlGaAs, InGaAs-InGaAsP, and GaInP- AlInP quantum well systems, and it is shown that low absorption losses are obtained after intermixing. Oxide stripe lasers with integrated slab waveguides have also enabled the production of a narrow single lobed far field pattern in both InGaAs-InAlGaAs, and GaInP-AlGaInP devices. Extended cavity ridge waveguide lasers operating at 1.5 micrometers are demonstrated with low loss waveguides, and it is shown that this loss is limited only by free carrier absorption in the waveguide cladding layers. In addition, the operation of intermixed multi-mode interference coupler lasers is demonstrated, where four GaAs-AlGaAs laser amplifiers are monolithically integrated to produce high output powers of 180 mW in a single fundamental mode. The results illustrate that the technique can routinely be used to fabricate low los optical interconnects and offers a very promising route toward photonic integration.
Unusual properties of two branched RNA's with circular and linear components (1985)

Irradiation with ultraviolet light was used to create two nonlinear RNA molecules. Circular potato spindle tuber viroid (PSTV) RNA was crosslinked at a single site to generate a figure eight-shaped molecule; 5S rRNA from HeLa cells was transformed into an alpha-shaped molecule with a small circular element and two arms (1). Crosslinked RNA's could be separated from their untreated counterparts by electrophoresis in polyacrylamide gels containing urea. The gel mobility of crosslinked PSTV was not altered by boiling, treatment with E. coli RNase III or glyoxalation. However, mild nuclease digestion ("nicking") produced derivatives which migrated more slowly than the starting material in gels of certain polyacrylamide concentrations, but not in others. Limited nuclease digestion of crosslinked 5S rRNA did not generate any detectable products with reduced mobility in the gels tested. Thus, the ability of the "nicking assay" to reveal circular elements within nonlinear RNA's can vary depending upon the composition of the gel chosen for analysis and on the size of the circular element relative to the rest of the molecule.
Circulating fluidized bed gasification of biomass resource: originality in system design and experimental approach (2001)

An innovative design concept for circulating fluidized bed (CFB) gasification of biomass and other solid wastes is presented. The concept combines and integrates partial oxidation, fast pyrolysis (with an instantaneous drying). gasification, and tar cracking. as well as a shift reaction, with the purpose of producing high quality or gas, in terms of low tar level and particulates carried out in the producer gas, and overall emissions reduction associated with producer gas combustion. The first-hand experiences of operating CFB gasification systems (CFBGs), in particular of keeping the operation in a stable and reliable state with the minimum fluctuations in the producer gas volume and composition are also of our focus.
An electrochemical capillary fill device for the analysis of glucose incorporating glucose oxidase and ruthenium (III) hexamine as mediator (1992)

Abstract This article describes a coulometric measurement device for glucose based on thin‐layer bulk electrolysis. The analysis is carried out in a specially constructed cell, the electrochemical capillary fill device, which has a total volume of less than 20μl. Once the sample enters the cell by capillary action, the freeze‐dried assay components (glucose oxidase, ruthenium (III) hexamine, buffer salts, etc.) become solubilized and quickly disperse throughout the volume of the cell. After a period of one min, the time taken for the enzyme catalyzed oxidation of glucose to gluconic acid to reach completion, a potential step is applied and the current transient, resulting from the oxidation of reduced mediator at the working electrode, integrated over a period of 60 s. From the resultant charge value, the concentration of glucose in the sample can be unambiguously determined. The response of the sensor is both linear and accurate over the range 2–30 mM, which covers the normally accepted range for blood glucose levels in diabetic patients. The second order rate constant for the reaction between reduced glucose oxidase and ruthenium (III) hexamine was evaluated by conducting a numerically based analysis that was designed to separate the diffusional and catatytic components of current transients.
[Experimental and clinical islets transplantation. Current status]. (1992)

25 years have passed since the first enzymatic isolation of islets of Langerhans from the rat pancreas. During this period of time, it could be demonstrated that transplantation of syngeneic islets intraportally into streptozoticin-treated diabetic recipients (rat, mouse) does not only guarantee long term normoglycemia but inhibits also typical late complications of the disease. Allogeneic islets, however, exhibit strong immunogenicity (rejection within a few days) which can be overcome by various immunomodulating in vitro measures of the islets before transplantation. Isolated islets have been successfully transplanted also in larger animals as dogs and pigs, when transplanted in an autologous or allogeneic system. In human diabetes the success rate of islet transplantation up to now is low and cannot be compared with the results in experimental diabetes. The reasons are manyfold: islet damage due to long ischemia time, low number of islets, low purity, lack of diagnostic markers which indicate rejection, autoimmune destruction. The fact that in the meantime a few patients remain insulin independent after a single islet transplant with the maximum of 2 years indicates however that this method in principle may serve as a tool for the treatment of diabetes. This is underlined by several advantages compared to pancreatic organ transplantation as low risk of the procedure for the recipient and the possibility of repeated transplantation. In addition, in the future xenotransplantation of (porcine) islets might be feasible.
Insight into the role of mTOR and metabolism in T cells reveals new potential approaches to preventing graft rejection (2014)

Initial studies focused on the ability of the mTOR inhibitor rapamycin to suppress immune responses by inhibiting T cell proliferation. Since then, both pharmacologic and genetic studies have revealed a central role for mTOR in regulating T cell activation, differentiation, and function independent of proliferation. Specifically, it has become clear that mTOR plays an important role in regulating the metabolic machinery necessary for effector, regulatory, and memory T cell generation. As such, direct inhibition of metabolism may emerge as a potent and selective means of preventing graft rejection. This review will discuss new insights regarding the ability of downstream signaling pathways, including mTOR-dependent metabolic pathways in regulating T cell responses. Finally, we will discuss these new insights in the context of developing novel immunoregulatory regimens for transplantation.
15-Deoxy-Δ 12,14 -prostaglandin J 2 inhibits multiple steps in the NF-κB signaling pathway (2000)

Prostaglandin J(2) (PGJ(2)) and its metabolites Delta(12)-PGJ(2) and 15-deoxy-Delta(12,14)-PGJ(2) (15d-PGJ(2)) are naturally occurring derivatives of prostaglandin D(2) that have been suggested to exert antiinflammatory effects in vivo. 15d-PGJ(2) is a high-affinity ligand for the peroxisome proliferator-activated receptor gamma (PPARgamma) and has been demonstrated to inhibit the induction of inflammatory response genes, including inducible NO synthase and tumor necrosis factor alpha, in a PPARgamma-dependent manner. We report here that 15d-PGJ(2) potently inhibits NF-kappaB-dependent transcription by two additional PPARgamma-independent mechanisms. Several lines of evidence suggest that 15d-PGJ(2) directly inhibits NF-kappaB-dependent gene expression through covalent modifications of critical cysteine residues in IkappaB kinase and the DNA-binding domains of NF-kappaB subunits. These mechanisms act in combination to inhibit transactivation of the NF-kappaB target gene cyclooxygenase 2. Direct inhibition of NF-kappaB signaling by 15d-PGJ(2) may contribute to negative regulation of prostaglandin biosynthesis and inflammation, suggesting additional approaches to the development of antiinflammatory drugs.
Recent Progress and Future Challenges in MR Electric Properties Tomography (2013)

MR Electric Properties Tomography (EPT) is a lately developed medical imaging modality capable of visualizing both conductivity and permittivity of the patient at the Larmor frequency using B 1 maps. The paper discusses the development of EPT reconstructions, EPT sequences, EPT experiments, and challenging issues of EPT.
Changing boundaries in the treatment of malignant gliomas (2001)

Malignant gliomas are still among the most lethal and difficult tumors to treat; even the most intensive combinations of radio- and chemotherapy are not curative and yield only a modest impact on survival for most of these patients, as long-term survivors are less than 10%. There is a major need for new chemotherapeutic drugs and alternative therapeutic modalities. This review aims to define the best standard treatment in the common clinical practice and also summarizes the most promising lines of investigational research in the field of neuro-oncology, which will probably offer new and long-awaited valid therapy options for brain tumor patients.
Identification of amino acid substitutions that alter the substrate specificity of TEM-1 beta-lactamase (1992)

TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Recently, TEM beta-lactamase variants with amino acid substitutions in the active-site pocket of the enzyme have been identified in natural isolates with increased resistance to extended-spectrum cephalosporins. To identify other amino acid substitutions that alter the activity of TEM-1 towards extended-spectrum cephalosporins, we probed regions around the active-site pocket by random-replacement mutagenesis. This mutagenesis technique involves randomizing the DNA sequence of three to six codons in the blaTEM-1 gene to form a library containing all or nearly all of the possible substitutions for the region randomized. In total, 20 different residue positions that had been randomized were screened for amino acid substitutions that increased enzyme activity towards the extended-spectrum cephalosporin cefotaxime. Substitutions at positions 104, 168, and 238 in the TEM-1 beta-lactamase that resulted in increased enzyme activity towards extended-spectrum cephalosporins were found. In addition, small deletions in the loop containing residues 166 to 170 drastically altered the substrate specificity of the enzyme by increasing activity towards extended-spectrum cephalosporins while virtually eliminating activity towards ampicillin.
The electronic broadsheet : all the news that fits the display (1991)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Architecture, 1991.