gebhart/patrepeval huggingface dataset:
Nucleic Acid Sequence-Based Amplification with Oligochromatography for Detection of Trypanosoma brucei in Clinical Samples (2008)

Molecular tools, such as real-time nucleic acid sequence-based amplification (NASBA) and PCR, have been developed to detect Trypanosoma brucei parasites in blood for the diagnosis of human African trypanosomiasis (HAT). Despite good sensitivity, these techniques are not implemented in HAT control programs due to the high cost of the equipment, which is unaffordable for laboratories in developing countries where HAT is endemic. In this study, a simplified technique, oligochromatography (OC), was developed for the detection of amplification products of T. brucei 18S rRNA by NASBA. The T. brucei NASBA-OC test has analytical sensitivities of 1 to 10 parasites/ml on nucleic acids extracted from parasite culture and 10 parasites/ml on spiked blood. The test showed no reaction with nontarget pathogens or with blood from healthy controls. Compared to the composite standard applied in the present study, i.e., parasitological confirmation of a HAT case by direct microscopy or by microscopy after concentration of parasites using either a microhematocrit centrifugation technique or a mini-anion-exchange centrifugation technique, NASBA-OC on blood samples had a sensitivity of 73.0% (95% confidence interval, 60 to 83%), while standard expert microscopy had a sensitivity of 57.1% (95% confidence interval, 44 to 69%). On cerebrospinal fluid samples, NASBA-OC had a sensitivity of 88.2% (95% confidence interval, 75 to 95%) and standard microscopy had a sensitivity of 86.2% (95% confidence interval, 64 to 88%). The T. brucei NASBA-OC test developed in this study can be employed in field laboratories, because it does not require a thermocycler; a simple heat block or a water bath maintained at two different temperatures is sufficient for amplification.
Apoptosis, oncosis, and necrosis. An overview of cell death. (1995)

The historical development of the cell death concept is reviewed, with special attention to the origin of the terms necrosis, coagulation necrosis, autolysis, physiological cell death, programmed cell death, chromatolysis (the first name of apoptosis in 1914), karyorhexis, karyolysis, and cell suicide, of which there are three forms: by lysosomes, by free radicals, and by a genetic mechanism (apoptosis). Some of the typical features of apoptosis are discussed, such as budding (as opposed to blebbing and zeiosis) and the inflammatory response. For cell death not by apoptosis the most satisfactory term is accidental cell death. Necrosis is commonly used but it is not appropriate, because it does not indicate a form of cell death but refers to changes secondary to cell death by any mechanism, including apoptosis. Abundant data are available on one form of accidental cell death, namely ischemic cell death, which can be considered an entity of its own, caused by failure of the ionic pumps of the plasma membrane. Because ischemic cell death (in known models) is accompanied by swelling, the name oncosis is proposed for this condition. The term oncosis (derived from ónkos, meaning swelling) was proposed in 1910 by von Reckling-hausen precisely to mean cell death with swelling. Oncosis leads to necrosis with karyolysis and stands in contrast to apoptosis, which leads to necrosis with karyorhexis and cell shrinkage.
Acute compartment syndrome (2000)

We have analysed associated factors in 164 patients with acute compartment syndrome whom we treated over an eight-year period. In 69% there was an associated fracture, about half of which were of the tibial shaft. Most patients were men, usually under 35 years of age. Acute compartment syndrome of the forearm, with associated fracture of the distal end of the radius, was again seen most commonly in young men. Injury to soft tissues, without fracture, was the second most common cause of the syndrome and one-tenth of the patients had a bleeding disorder or were taking anticoagulant drugs. We found that young patients, especially men, were at risk of acute compartment syndrome after injury. When treating such injured patients, the diagnosis should be made early, utilising measurements of tissue pressure.
Chronic vagus nerve stimulation: a new and promising therapeutic approach for chronic heart failure (2010)

This open-label study shows that chronic VNS in CHF patients with severe systolic dysfunction may be safe and tolerable and may improve quality of life and LV function. A controlled clinical trial appears warranted.
Gas storage in porous metal–organic frameworks for clean energy applications (2009)

Depletion of fossil oil deposits and the escalating threat of global warming have put clean energy research, which includes the search for clean energy carriers such as hydrogen and methane as well as the reduction of carbon dioxide emissions, on the urgent agenda. A significant technical challenge has been recognized as the development of a viable method to efficiently trap hydrogen, methane and carbon dioxide gas molecules in a confined space for various applications. This issue can be addressed by employing highly porous materials as storage media, and porous metal-organic frameworks (MOFs) which have exceptionally high surface areas as well as chemically-tunable structures are playing an unusual role in this respect. In this feature article we provide an overview of the current status of clean energy applications of porous MOFs, including hydrogen storage, methane storage and carbon dioxide capture.
Macrolide Resistance Conferred by Base Substitutions in 23S rRNA (2001)

Resistance to all major groups of antibiotics has arisen hand in hand with their extensive use in medicine and animal husbandry, and macrolide antibiotics are no exception.The therapeutic utility of macrolides has been severely compromised by the emergence of drug resistance in many pathogenic bacteria.
Animal Pneumoviruses: Molecular Genetics and Pathogenesis (2004)

Pneumoviruses are single-stranded, negative-sense, nonsegmented RNA viruses of the family Paramyxoviridae, subfamily Pneumovirinae, and include pathogens that infect humans (respiratory syncytial virus and human metapneumovirus), domestic mammals (bovine, ovine, and caprine respiratory syncytial viruses), rodents (pneumonia virus of mice), and birds (avian metapneumovirus). Among the topics considered in this review are recent studies focused on the roles of the individual virus-encoded components in promoting virus replication as well as in altering and evading innate antiviral host defenses. Advances in the molecular technology of pneumoviruses and the emergence of recombinant pneumoviruses that are leading to improved virus-based vaccine formulations are also discussed. Since pneumovirus infection in natural hosts is associated with a profound inflammatory response that persists despite adequate antiviral therapy, we also review the recent experimental treatment strategies that have focused on combined antiviral, anti-inflammatory, and immunomodulatory approaches.
Possible Compartmental Cytokine Release Syndrome in a Patient With Recurrent Ovarian Cancer After Treatment With Mesothelin-targeted CAR-T Cells (2017)

Cytokine release syndrome (CRS) is a potentially severe systemic toxicity seen after adoptive T-cell therapy and caused by T-cell activation and proliferation and is associated with elevated circulating levels of cytokines such as C-reactive protein, interleukin-6 (IL-6), and interferon-γ and has previously been described as a systemic response in hematologic malignancies. A 52-year-old woman with BRCA 1 mutation positive heavily pretreated advanced recurrent serous ovarian cancer was treated under a compassionate use protocol with autologous mesothelin-redirected chimeric antigen receptor T cells (CART-meso). Autologous T cells were transduced to express a receptor composed of an extracellular antimesothelin single-chain variable fragment fused to 4-1BB and TCR-zeta signaling domain. This patient was infused with 3×10 CART-meso T cells/m without lymphodepletion and developed compartmental CRS confined to the pleural cavities. The compartmental CRS was evidenced by an increase in IL-6 and accumulation of CART-meso T cells in pleural fluid compared with peripheral blood and was successfully treated the anti-IL6 receptor antagonist tocilizumab on D21 after the T-cell infusion. This is the first description of a compartmental CRS in a patient with solid malignancy. This response could be due to malignant pleural fluid creating an environment where T cells could interact with tumor cells and suggests localized on-target CAR-T-cell activation.
Chromogenic Charge Transfer Cleft-Type Tetrahydrobenzoxanthene Enantioselective Receptors for Dinitrobenzoylamino Acids (2004)

A combination of a benzoxanthene cleft-type receptor with an electron-rich aromatic ring capable of establishing charge-tranfer interactions provides enantioselective receptors for dinitrobenzoylamino acids. Racemic mixtures of the receptor can be resolved with TLCs impregnated with the guest. The structure of the complexes has been established in an X-ray study. Enantiomeric amino acids provide complexes with different colors.
Orientation studies in polyacrylonitrile films uniaxially drawn in the solid state (1994)

Abstract Polyacrylonitrile (PAN) films were made by casting a dimethyl sulphoxide (DMSO) solution. After drying, the films were uniaxially drawn by an essentially solid‐state drawing procedure. Using polarised‐infrared (IR) spectroscopy, the dichroism of the nitrile‐stretching vibration was monitored as a function of draw ratio. The dichroism results were converted to plots of chain‐orientation factor versus draw ratio. For this, α, the transition‐moment angle of the vibration, has to be known. Though a value of 68–73° has been suggested in the literature, for the present samples α cannot be 70° or less, and 73° is the most appropriate. The meaning and nature of the transition‐moment angle in the context of a flexible‐chain polymer molecule is discussed. The IR spectrum also showed dichroism in the SO stretch and the CH 3 rocking vibrations from the (residual) DMSO present in the film, indicating that the solvent molecules were also orientated. It is proposed that this occurred due to dipolar interactions between the SO and the CN groups, which led to solvent molecules being bound to the polymer chains. X‐ray diffraction studies indicated ‘lateral‐ordering’ consisting of hexagonally packed, rod‐like chains with no c ‐axis order. The diffraction patterns obtained here were the ‘standard’ ones for PAN, in contrast to those observed previously in solvent‐containing PAN gels.
Patterning PDMS using a combination of wet and dry etching (2009)

PDMS films of 10 μm thickness can be patterned within 30 min by combining dry etching to achieve substantially vertical sidewalls with wet etching to achieve high etch rates and to protect the underlying substrate from attack. Dry etching alone would have taken 5 h, and wet etching alone would produce severe undercutting. In addition, using either technique alone produces undesirable surface morphologies. The mask used during etching is critical to a successful patterning outcome. E-beam evaporated Al was found to work well, adhering strongly to oxygen-plasma-treated PDMS and holding up well during both dry and wet etching. To prevent wrinkling of the PDMS, a fast deposition rate should be used. (Some figures in this article are in colour only in the electronic version)
Light‐Triggered Multifunctionality at Surfaces Mediated by Photolabile Protecting Groups (2012)

Photoremovable protecting groups (PRPGs) are applied to organic surfaces, thin polymer films, and hydrogels to achieve light-based remote control of their (bio)chemical and physical properties. These can be localized (i.e. patterned), tunable by exposure dose, and generated on-demand. Using PRPGs with independent response to different wavelengths, multifunctional materials with a number of individually addressable functional states can be generated. Light-triggered polymerization, crosslinking, and degradation processes as well as release of attached molecules can be realized. Light-responsive surfaces and materials based on PRPGs open interesting possibilities for the next generation of instructive materials for cell culture and tissue regeneration.
A non-covalent peptide-based strategy for siRNA delivery (2007)

The major obstacle to clinical development of siRNAs (short interfering RNAs), like for most of the nucleic-acid-based strategies, is their poor cellular uptake and bioavailability. Although several viral and non-viral strategies have been proposed to improve siRNA delivery, their applications in vivo remain a major challenge. We have developed a new strategy, based on a short amphipathic peptide, MPG, that is able to form stable nanoparticles with siRNA. MPG-based particles enter the cell independently of the endosomal pathway and can efficiently deliver siRNA in a fully biologically active form into a variety of cell lines and in vivo. This short review will discuss the mechanism and the potency of the MPG strategy for siRNA delivery both in vitro and in vivo.
The Rossmann Fourier autoindexing algorithm in MOSFLM (1999)

The fast Fourier transform (FFT) autoindexing routines written by the Rossmann group at Purdue University have been incorporated in MOSFLM, providing a rapid and reliable method of indexing oscillation images. This is a procedure which extracts direct-space information about the unit cell from the FFT. The method and its implementation in MOSFLM are discussed.
Total synthesis of (+)-leinamycin (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of (+)-leinamycinYutaka Kanda and Tohru FukuyamaCite this: J. Am. Chem. Soc. 1993, 115, 18, 8451–8452Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://doi.org/10.1021/ja00071a066RIGHTS & PERMISSIONSArticle Views1861Altmetric-Citations122LEARN 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 InReddit PDF (248 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
RECONSTRUCTION OF REAL-WORLD OBJECTS VIA SIMULTANEOUS REGISTRATION AND ROBUST COMBINATION OF MULTIPLE RANGE IMAGES (1997)

Range finder devices are quite useful to measure the geometry of real-world objects. However, the reconstruction of large and complicated objects often requires the acquisition of multiple range images showing different views of the object. With our reconstruction method, the relative orientations of all range images are determined via simultaneous registration of all range images. The registration process is based on a least-squares approach where a distance metric between the overlapping range images is minimized. Registration errors are not accumulated, and it is even possible to reconstruct large objects from an arbitrary number of small range images. A resolution hierarchy accelerates the registration substantially. In order to exploit redundancies, the overlapping surfaces are optimally adapted to each other. The processed range images are converted to a signed distance function, which is based on the idea that no part of the object can lie between the scanner and the measured su rface in any view. According to the signed distance function an intermediate volumetric model is sculptured out and polygnalized with isosurface techniques. The accuracy of the generated mesh is improved by moving its vertices onto the surface implicitly defined bt the registered range images.
Long-chain conversion of [13C]linoleic acid and α-linolenic acid in response to marked changes in their dietary intake in men (2004)

We studied the long-chain conversion of [U-13C]alpha-linolenic acid (ALA) and linoleic acid (LA) and responses of erythrocyte phospholipid composition to variation in the dietary ratios of 18:3n-3 (ALA) and 18:2n-6 (LA) for 12 weeks in 38 moderately hyperlipidemic men. Diets were enriched with either flaxseed oil (FXO; 17 g/day ALA, n=21) or sunflower oil (SO; 17 g/day LA, n=17). The FXO diet induced increases in phospholipid ALA (>3-fold), 20:5n-3 [eicosapentaenoic acid (EPA), >2-fold], and 22:5n-3 [docosapentaenoic acid (DPA), 50%] but no change in 22:6n-3 [docosahexanoic acid (DHA)], LA, or 20:4n-6 [arachidonic acid (AA)]. The increases in EPA and DPA but not DHA were similar to those in subjects given the SO diet enriched with 3 g of EPA plus DHA from fish oil (n=19). The SO diet induced a small increase in LA but no change in AA. Long-chain conversion of [U-13C]ALA and [U-13C]LA, calculated from peak plasma 13C concentrations after simple modeling for tracer dilution in subsets from the FXO (n=6) and SO (n=5) diets, was similar but low for the two tracers (i.e., AA, 0.2%; EPA, 0.3%; and DPA, 0.02%) and varied directly with precursor concentrations and inversely with concentrations of fatty acids of the alternative series. [13C]DHA formation was very low (<0.01%) with no dietary influences.
Tissue-Specific Promoters Regulate Aromatase Cytochrome P450 Gene Expression in Human Ovary and Fetal Tissues (1991)

The formation of estrogens from C19 steroids is catalyzed by a specific form of cytochrome P450, aromatase cytochrome P450 (P450AROM; the product of the CYP19 gene). Previous studies have demonstrated that aromatase activity in human adipose and ovarian granulosa cells is subject to complex multifactorial regulation and that changes in activity are correlated with changes in the levels of mRNA encoding P450AROM. We have previously isolated the human CYP19 gene. Two unique untranslated first exons (exons I.1 and I.2) have been identified in mRNA specific for P450AROM in human placenta. Although the proportion of transcripts encoding exon I.2 is very small, genomic clones encoding the sequences of both exons I.1 and I.2 have recently been isolated. The corpus luteum of human ovary differs in that promoters I.1 and I.2 are completely inactive. Sequence analysis of the DNA immediately 5' of exon II (which contains the start site of translation) demonstrates the presence of a TATAA sequence beginning 149 basepairs 5' of the ATG initiation codon identified in placental exon II. Using a combination of primer extension and S1 nuclease protection analysis, it appears that the initiation site of ovarian P450AROM transcripts aligns 26 basepairs down-stream of the sequence TATAA. It appears, therefore, that the expression of P450AROM-specific mRNA in corpus luteum is regulated by an additional promoter (promoter II), which is located just 5' of exon II. Consistent with these observations, Northern analysis of poly(A)+ RNA isolated from placenta and corpus luteum demonstrates that the major promoter of placental P450AROM is promoter I.1, while the major promoter in the corpus luteum is promoter II.(ABSTRACT TRUNCATED AT 250 WORDS)
Gabapentin and Pregabalin Can Interact Synergistically with Naproxen to Produce Antihyperalgesia (2002)

These data suggest that gabapentin + naproxen and pregabalin + naproxen can interact synergistically or additively to reverse thermal hyperalgesia associated with peripheral inflammation. Therefore, the use of gabapentin or pregabalin in low-dose combinations with naproxen may afford therapeutic advantages for clinical treatment of persistent inflammatory pain.
Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates (2010)

5-Hydroxymethylcytosine (hmC) was recently detected as the sixth base in mammalian tissue at so far controversial levels. The function of the modified base is currently unknown, but it is certain that the base is generated from 5-methylcytosine (mC). This fuels the hypothesis that it represents an intermediate of an active demethylation process, which could involve further oxidation of the hydroxymethyl group to a formyl or carboxyl group followed by either deformylation or decarboxylation. Here, we use an ultra-sensitive and accurate isotope based LC-MS method to precisely determine the levels of hmC in various mouse tissues and we searched for 5-formylcytosine (fC), 5-carboxylcytosine (caC), and 5-hydroxymethyluracil (hmU) as putative active demethylation intermediates. Our data suggest that an active oxidative mC demethylation pathway is unlikely to occur. Additionally, we show using HPLC-MS analysis and immunohistochemistry that hmC is present in all tissues and cell types with highest concentrations in neuronal cells of the CNS.
Double target for tumor mass destruction (2003)

failure are progressive, it suggests that this counter-regulatory mechanism within the heart is limited and ultimately fails to provide long-term protection.Secondly, we must consider whether or not it will ultimately be beneficial or detrimental to treat (i.e., prevent) cardiac hypertrophy in response to pathologic conditions such as hypertension or valvular disease.In other words, would cardiac decompensation simply occur sooner if one blocks the hypertrophic phase of the response?
A quarter-micron planarized interconnection technology with self-aligned plug (1992)

In order to realize minimum pitch interconnections without degrading reliability, self-aligned contacts (SACs) between interconnections and plugs are necessary. The planarized interconnections with SAC plugs is formed for quarter-micron size as follows. Interconnection trenches and contact holes are formed using a self-aligned etch-stop layer, followed by simultaneous metal-filling into the trenches and contact holes. Si-rich oxide (SRO) films are found to be promising for a self-aligned etch-stop layer with their high etching selectivity to SiO/sub 2/ as high as 10-30. Sufficiently low line resistance of 15 k Omega /cm and low contact resistance of 70 Omega /contact are obtained with the quarter-micron W-interconnection with the SAC plugs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Autoreactive T and B cells responding to myelin proteolipid protein in multiple sclerosis and controls (1991)

The pathogenesis of multiple sclerosis (MS) could involve an autoimmune response to proteolipid protein (PLP). Immunization of experimental animals with this major myelin protein can lead to experimental allergic encephalomyelitis. To identify a possible role of PLP as target antigen in MS, we evaluated T cell immunity to PLP in blood and cerebrospinal fluid (CSF) from patients with MS and controls by counting cells which in response to PLP in short-term cultures secreted interferon-gamma. The PLP-specific B cell response was analyzed by counting cells secreting anti-PLP antibodies. PLP-reactive T cells were detected in blood of most MS patients (mean value 1 per 20,408 mononuclear cells), and at 41-fold higher numbers in CSF (mean 1 per 500 CSF cells). Anti-PLP IgG antibody-secreting cells were detected in blood from most MS patients (mean 1 per 30,303 cells), but such cells were 49-fold more frequent in CSF (mean 1 per 625 cells). PLP-reactive T and B cells were also detected in blood and CSF from control patients, but at much lower numbers. A strong and persistent autoimmune response to PLP as well as to other myelin proteins, enriched in CSF, is proposed to be pathogenetically important in MS.