gebhart/patrepeval huggingface dataset:
Genetic characterization of new varieties and hybrids of citrus table fruit through isoenzymes (2003)

The aim of this study was to establish isoenzymatic patterns to genetically characterize the orange varieties ‘Lane Late’, ‘Navalete’, ‘Navelina’ and ‘Salustiana’, mandarin varieties ‘Clemenules’, ‘Marisol’ and ‘Satsuma Okitsu’, and the hybrids ‘Nova’ and ‘Ortanique’. The following isoenzymatic systems were utilized: alcohol dehydrogenase (ADH), esterase (EST), acid phosphatase (APS), phosphoglucoisomerase (PGI), phosphoglucomutase (PGM), 6-phosphogluconate dehydrogenase (6-PGDH), glutamate oxaloacetate transaminase (GOT), isocitrate dehydrogenase (IDH), leucine aminopeptidase (LAP), malate dehydrogenase (MDH), peroxidase (PRX), sorbitol dehydrogenase (SDH), superoxidase dismutase (SOD) and shikimate dehydrogenase (SKDH). Proteins were extracted from leaves and the isoenzymatic polymorphisms were analyzed by polyacrylamide gel electrophoresis. The PGM isoenzyme showed the highest differentiation among the genetic materials tested. The banding profiles observed for PGM, SKDH and EST were satisfactory to characterize the mandarin varieties and hybrids studied. However, no polymorphic bands were found in sweet oranges with the 14 isoenzymes tested.
An origin of the immunogenicity of in vitro transcribed RNA (2018)

The emergence of RNA-based therapeutics demands robust and economical methods to produce RNA with few byproducts from aberrant activity. While in vitro transcription using the bacteriophage T7 RNA polymerase is one such popular method, its transcripts are known to display an immune-stimulatory activity that is often undesirable and uncontrollable. We here showed that the immune-stimulatory activity of T7 transcript is contributed by its aberrant activity to initiate transcription from a promoter-less DNA end. This activity results in the production of an antisense RNA that is fully complementary to the intended sense RNA product, and consequently a long double-stranded RNA (dsRNA) that can robustly stimulate a cytosolic pattern recognition receptor, MDA5. This promoter-independent transcriptional activity of the T7 RNA polymerase was observed for a wide range of DNA sequences and lengths, but can be suppressed by altering the transcription reaction with modified nucleotides or by reducing the Mg2+ concentration. The current work thus not only offers a previously unappreciated mechanism by which T7 transcripts stimulate the innate immune system, but also shows that the immune-stimulatory activity can be readily regulated.
Extracting information from cDNA arrays (2001)

High-density DNA arrays allow measurements of gene expression levels (messenger RNA abundance) for thousands of genes simultaneously. We analyze arrays with spotted cDNA used in monitoring of expression profiles. A dilution series of a mouse liver probe is deployed to quantify the reproducibility of expression measurements. Saturation effects limit the accessible signal range at high intensities. Additive noise and outshining from neighboring spots dominate at low intensities. For repeated measurements on the same filter and filter-to-filter comparisons correlation coefficients of 0.98 are found. Next we consider the clustering of gene expression time series from stimulated human fibroblasts which aims at finding co-regulated genes. We analyze how preprocessing, the distance measure, and the clustering algorithm affect the resulting clusters. Finally we discuss algorithms for the identification of transcription factor binding sites from clusters of co-regulated genes. (c) 2001 American Institute of Physics.
Minimized protein structures: A little goes a long way (1997)

In this issue of the Proceedings , Starovasnik, Braisted, and Wells (1) present the solution structure of synthetic peptides that are half the size of their natural counterpart, but nonetheless maintain well ordered structures and bind tightly to their natural target site. Small protein domains that are structurally stable and functionally active serve as attractive models for studies of protein folding and as starting points for drug design.

Minimized protein domains were selected by Braisted and Wells (2) solely by the domains’ ability to bind to the target site, the constant region of G-type immunoglobulins (IgG). The current paper demonstrates that despite their small size, these miniature binding proteins form well ordered structures that closely resemble the binding motif in the larger natural protein. The similarity between the observed structures and the intended target structure validates the protein minimization strategy and demonstrates that proteins can be designed to do more with less.

The sequences studied by Starovasnik, Braisted, and Wells are derived from combinatorial libraries evolved in vitro (1, 2). Combinatorial methods recently have revolutionized the discovery of new molecules in the laboratory (3). However, combinatorial approaches have been used by nature for eons to evolve new sequences capable of folding into stable structures and performing essential functions. With time and resources that are virtually unlimited, nature can successfully select folded proteins from combinatorial libraries generated entirely at random (4). Compared with nature, laboratory scientists are at a decided disadvantage: With limited resources and far less patience, we can neither sample sequence diversity as extensively nor wait as long. To succeed in the laboratory, we must depart from nature’s random approach; we must incorporate elements of rational design to constrain our synthetic libraries to those regions of sequence space most likely to yield desired molecules. For example, merely constraining …
Epidermal Growth Factor Receptor Variant III Contributes to Cancer Stem Cell Phenotypes in Invasive Breast Carcinoma (2012)

EGFRvIII is a tumor-specific variant of the epidermal growth factor receptor (EGFR). Although EGFRvIII is most commonly found in glioblastoma, its expression in other tumor types remains controversial. In this study, we investigated EGFRvIII expression and amplification in primary breast carcinoma. Our analyses confirmed the presence of EGFRvIII, but in the absence of amplification or rearrangement of the EGFR locus. Nested reverse transcriptase PCR and flow cytometry were used to detect a higher percentage of positive cases. EGFRvIII-positive cells showed increased expression of genes associated with self-renewal and epithelial-mesenchymal transition along with a higher percentage of stem-like cells. EGFRvIII also increased in vitro sphere formation and in vivo tumor formation. Mechanistically, EGFRvIII mediated its effects through the Wnt/β-catenin pathway, leading to increased β-catenin target gene expression. Inhibition of this pathway reversed the observed effects on cancer stem cell (CSC) phenotypes. Together, our findings show that EGFRvIII is expressed in primary breast tumors and contributes to CSC phenotypes in breast cancer cell lines through the Wnt pathway. These data suggest a novel function for EGFRvIII in breast tumorigenesis.
Therapeutic efficacy of humanized recombinant anti–interleukin‐6 receptor antibody in children with systemic‐onset juvenile idiopathic arthritis (2005)

MRA treatment of children with active systemic disease results in clinical improvement and in normalized levels of acute-phase reactants. MRA was safe and well tolerated and provided greater clinical benefit than conventional corticosteroids, considering the ill effects of IL-6 and adverse events.
Look who's talking: speaker detection using video and audio correlation (2002)

The visual motion of the mouth and the corresponding audio data generated when a person speaks are highly correlated. This fact has been exploited for lip/speech-reading and for improving speech recognition. We describe a method of automatically detecting a talking person (both spatially and temporally) using video and audio data from a single microphone. The audio-visual correlation is learned using a time-delayed neural network, which is then used to perform a spatio-temporal search for a speaking person. Applications include videoconferencing, video indexing and improving human-computer interaction (HCI). An example HCI application is provided.
Ultimate efficiency of polymer/fullerene bulk heterojunction solar cells (2006)

We present model calculations to explore the potential of polymer/fullerene bulk heterojunction solar cells. As a starting point, devices based on poly(3-hexylthiophene) and 6,6-phenyl C61-butyric acid methyl ester (PCBM), reaching 3.5% efficiency, are modeled. Lowering the polymeric band gap will lead to a device efficiency exceeding 6%. Tuning the electronic levels of PCBM in such a way that less energy is lost in the electron transfer process enhances the efficiency to values in excess of 8%. Ultimately, with an optimized level tuning, band gap, and balanced mobilities polymeric solar cells can reach power conversion efficiencies approaching 11%.
Insertional mutagenesis identifies a member of the Wnt gene family as a candidate oncogene in the mammary epithelium of int-2/Fgf-3 transgenic mice. (1995)

Transgenic mice harboring the int-2/Fgf-3 protooncogene under transcriptional control of the mouse mammary tumor virus (MMTV) promoter/enhancer exhibit a dramatic, benign hyperplasia of the mammary gland. In one int-2 transgenic line (TG.NX), this growth disturbance is evoked by pregnancy and regresses after parturition. Regression of hyperplastic mammary epithelium is less complete after successive pregnancies, and, within 10 months, most TG.NX mice stochastically develop mammary carcinomas that are transplantable in virgin, syngeneic mice. To identify genes that cooperate with int-2 in cell transformation, we infected TG.NX transgenic mice with MMTV. In a cohort of 14 animals, most mammary tumors represented clonal or oligoclonal outgrowths harboring one to five proviral MMTV integrants. Eight of 35 (23%) MMTV+ tumors exhibited proviral insertion at the Wnt-1 locus. No provirus was detected at the int-2, int-3, or Wnt-3 loci. By Southern analysis, two tumors had proviral insertions at the same genomic location, which was mapped to chromosome 15. Cloning of this int locus identified an additional member of the Wnt gene family. The predicted 389-amino acid protein is most closely related to zebrafish Wnt-10a (58% amino acid identity over 362 residues) and, based on homology analysis, was designated Wnt-10b. This newly discovered Wnt family member was expressed in the embryo and mammary gland of virgin but not pregnant mice and represents a candidate collaborating oncogene of int-2/Fgf-3 in the mammary epithelium.
Chaining model transformations (2012)

Model transformation is one of the key practices of Model-Driven Engineering. Building very large model transformations may benefit from the construction of small transformations, in order to manage complexity and enhance reusability, maintainability and modularity. The decomposition of transformations into smaller ones raises the issue of assuring the validity of a composition: if two or more transformations are chained together, are the results of executing the chain the expected ones?
A practical algorithm for the determination of phase from image and diffraction plane pictures (1972)

An algorithm is presented for the rapid solution of the phase of the complete wave function whose intensity in the diffraction and imaging planes of an imaging system are known. A proof is given showing that a defined error between the estimated function and the correct function must decrease as the algorithm iterates. The problem of uniqueness is discussed and results are presented demonstrating the power of the method.
Tandem mass spectrometry in the clinical analysis of variant hemoglobins (1990)

A combination of mass spectrometric techniques (electrospray mass spectrometry, liquid secondary-ion mass spectrometry (LSIMS), tandem mass spectrometry) has been used for variant hemoglobin detection and characterization. Electrospray mass spectrometry allowed analysis of mixtures of intact globins giving the molecular weights (accuracy 1-2 Da), and information about relative amounts of globins present, simultaneously. Abnormal hemoglobins detected in this way and by other means (screening, clinical symptoms) were fractionated by C-4 reverse phase high-performance liquid chromatography (HPLC), and the separated globin chains (or the mixture of whole precipitated globin) were digested with trypsin. The tryptic peptides were separated by C-18 reverse phase HPLC and analysed by LSIMS to narrow down the mutation site to a single peptide. In some instances, the molecular weight of a variant peptide was sufficient to determine the mutation uniquely. When molecular weight information alone was insufficient to identify the mutation and its site, the peptide was sequenced by tandem mass spectrometry on a 4-sector instrument. In cases where more than one possible mutation site was present in the peptide and the mutation resulted in a change of only 1 Da in the peptide mass, the resolution and mass measurement accuracy of the 4-sector machine were essential in determining the correct sequence. The practical application of the methodologies presented is illustrated by the identification and analysis of Hb G-San Jose, Hb Willamette and D-Iran.
Design, Synthesis, and Imaging of Small Amphiphilic Rhenium and 99mTechnetium Tricarbonyl Complexes (2009)

The design, synthesis, radiolabeling, evaluation of stability, and in vivo investigation are presented of three variably charged, novel, short C(8) chain derivatized chelators for the [M(CO)(3)](+) core (M = (99m)Tc or Re). Labeling with [(99m)Tc(CO)(3)](+) showed complex formation in under 1 h reaction time and high stability toward 24 h histidine and cysteine challenges, as well as distinctive log P values for each complex. Distinct localization of small amphiphilic molecules in in vivo systems depends on the charge of the polar moiety and was studied via biodistribution (4 h) and imaging (15 min, 1, 2, and 4 h) in female C57Bl/6 mice.
Constraints in antigen processing result in unresponsiveness to a T cell epitope of hen egg lysozyme in C57BL/6 mice (1992)

T cell hybridoma clones were derived after fusion of BW-5147 parent cells with lymphocytes from C57BL/6 mice injected with phosphorylcholine (PC)-hen egg lysozyme (HEL) conjugates. Several T cell hybridomas were preferentially reactive with PC-HEL over unconjugated HEL, and a particular clone (PC-H4.1) was further analyzed. This T cell hybridoma clone could respond to its maximal level toward unconjugated HEL only when the dose of HEL was increased to 5-10-fold of the PC-HEL concentration. Interestingly, this clone was not stimulated by unfolded HEL (by S-carboxymethylation) to the level of PC-HEL. A synthetic peptide representing the amino acid position 47-61 of HEL, which is known to be non-immunogenic upon HEL injection in C57BL/6 mice, was able to stimulate the hybridoma only to a level comparable to that induced by unconjugated HEL. The T cell response to this synthetic peptide required an additional antigen-processing step, based on its inability to stimulate T cells after treatment of antigen-presenting cells with leupeptin, chloroquine or paraformaldehyde. Deletion of a single C-terminal amino acid residue of HEL 47-61 (arginine) significantly enhanced (10-100-fold of HEL 47-61) the T cell reactivity and abrogated the necessity of further antigen processing. These results suggest that the lack of a T cell response to a certain epitope may not be due to the lack of a T cell repertoire reactive to the epitope. In some cases, the unresponsiveness may be due to the difficulty in generating the particular epitopes. Taken together, modification of the lysozyme molecule with PC conjugation may facilitate further antigen processing of HEL to generate an optimal epitope for the nonresponder mice.
Bcl11a Deficiency Leads to Hematopoietic Stem Cell Defects with an Aging-like Phenotype (2016)

B cell CLL/lymphoma 11A (BCL11A) is a transcription factor and regulator of hemoglobin switching that has emerged as a promising therapeutic target for sickle cell disease and thalassemia. In the hematopoietic system, BCL11A is required for B lymphopoiesis, yet its role in other hematopoietic cells, especially hematopoietic stem cells (HSCs) remains elusive. The extensive expression of BCL11A in hematopoiesis implicates context-dependent roles, highlighting the importance of fully characterizing its function as part of ongoing efforts for stem cell therapy and regenerative medicine. Here, we demonstrate that BCL11A is indispensable for normal HSC function. Bcl11a deficiency results in HSC defects, typically observed in the aging hematopoietic system. We find that downregulation of cyclin-dependent kinase 6 (Cdk6), and the ensuing cell-cycle delay, correlate with HSC dysfunction. Our studies define a mechanism for BCL11A in regulation of HSC function and have important implications for the design of therapeutic approaches to targeting BCL11A.
Cholesterol crystal embolization in rat brain: a model for atheroembolic cerebral infarction. (1980)

Acute and delayed effects of embolizing cerebral surface vessels with cholesterol crystals were studied by direct observation in anesthetized rats and rabbits, using an open-skull technique, and by histological examination of brains at intervals of one day and one week following embolization. The number and size spectrum of crystals, which were infused into the ipsilateral internal carotid artery, were believed to approximate those released by a rupturing large atheromatous plaque in man, but the other lipid materials contained in such plaques were intentionally excluded. It was found that cholesterol crystals had only limited ability to impede blood flow in the 20--80 mu diameter arteries in view. They were also inert within the lumen, causing no vessel wall reaction even after a week; nor was any evidence seen of a thrombogenic effect. Local caliber changes in the containing artery were reproducibly seen, with dilatation of the arterial segment proximal to the embolus and narrowing of the segment in front. These changes appeared to represent an active response of the vessel wall, rather than a passive response to alterations in intraluminal pressure. The difficulty in subsequently locating cholesterol emboli histologically was confirmed. Possible therapeutic implications for atheroembolic cerebral infarction in man were discussed.
Inhibition of factor XIII activation by an anti-peptide monoclonal antibody (1991)

As the final enzyme in the coagulation cascade, activated fibrin stabilizing factor or factor XIII catalyzes the intermolecular cross-linking of fibrin chains. To study this enzyme in plasma, we derived a monoclonal antibody (MAb 309) against a peptide sequence (NH2-G-V-N-L-Q-E-F-C-COOH) in the thrombin activation site of factor XIII. Radioimmunoassays indicate that MAb 309 binds specifically to both platelet and plasma factor XIII. Peptide inhibition studies demonstrate that the MAb binds equally well to the factor XIII (FXIII) zymogen and the active form of FXIII (FXIIIa). In immunoblots of whole platelet lysates, MAb 309 binds only to FXIII and does not cross-react with other proteins. In saturation binding studies, the antibody shows a binding avidity of (1.75 +/- 0.35) x 10(9) M-1. MAb 309 also inhibited 99% of apparent FXIIIa activity in a standard transglutaminase assay. SDS-PAGE analysis of fibrin clots showed that MAb 309 inhibited fibrin gamma-gamma cross-linking. Moreover, MAb 309 accelerated the lysis of plasma clots, consistent with inhibition of fibrin-fibrin and fibrin-alpha 2-antiplasmin cross-linking. Immunoblotting experiments revealed that MAb 309 affected apparent FXIIIa activity by inhibiting the thrombin activation of the FXIII zymogen. In addition to its utility as a specific probe for the FXIII a-subunit, the strategy used to obtain MAb 309 may be used to generate MAbs that inhibit the activation of other coagulation factor zymogens.
Abbott's asylum seeker turn-back policy is a bad joke (2012)

For a few weeks in 2001 during the high-intensity Operation Relex period, Navy border protection vessel commanders were under standing orders from the Howard Government to attempt to turn back or tow back asylum seeker boats to Indonesia whenever they (or their senior onshore ADF commanders - it was never clear where such decisions were made) judged this could safely be achieved.
Creating Toolpaths Without Starts and Stops for Extrusion-Based Systems (2019)

Toolpath generation for extrusion-based additive manufacturing systems, called slicing, involves operations on polygonal contours that are derived from an STL file. Slicing generates multiple paths per layer (both closed-loop and open-loop) that are designed to optimally fill the space outlined by the polygon(s). In the course of printing a layer, the extruder must start and stop, the tip must be wiped, and the extruder must travel between paths without printing. Any amount of time the printer spends moving without printing is considered wasted time because the part isn’t being constructed. In addition, the start/stop point, known as the seam, is often a blemish on the surface of the part that contributes to weaker material properties. Therefore, a single path for creating multi-bead walled structures is desirable because it would save machine time and create parts with better surface finish. This paper will cover one method of modifying the CAD file and slicing engine to allow for parts to be printed without starting and stopping the extruder.
Aromatic Amino Acids and Modification of Parkinsonism (1967)

THE known biochemical abnormalities in Parkinson's disease consist of a decrease of melanin pigment in the substantia nigra1 , 2 and a decrease of some biogenic amines in the substantia nigra and the corpus striatum.3 These 2 defects might be interrelated, as suggested by the fact that in both melanocytes4 and sympathetic cells5 tyrosine is hydroxylated to dihydroxyphenylalanine, a common precursor in the synthesis of both melanin and catecholamines. Furthermore, both melanocytes and sympathetic cells originate from the neural crest.6 It was suggested earlier7 , 8 that the interrelations between melanogenesis and extrapyramidal disease might be of fundamental importance. It was noted that chronic . . .
New Multimeric Magnetic Resonance Imaging Agents (1998)

Approaches aimed at enhancing relaxivity by modulating the water relaxation time, tau m, will be important for the future development of functional MRI contrast agents for the imaging of biochemical processes.