gebhart/patrepeval huggingface dataset:
Progression of Age-Related Macular Degeneration (2003)

Among individuals with the early or intermediate stages of AMD, total and specific types of fat intake, as well as some fat-containing food groups, modified the risk of progression to advanced AMD. Fish intake and nuts reduced risk. Since advanced AMD is associated with visual loss and reduced quality of life, these preventive measures deserve additional research and greater emphasis.
Building extraction from high resolution satellite imagery based on multi-scale image segmentation and model matching (2008)

In this paper, we established a new general semiautomatic building rooftop extraction method applied for high resolution satellite imagery. Based on investigation of the current existed methods for building extraction and its feature extraction, a general framework of building rooftop extraction is proposed. To extract the precise building roof boundary, an seeded region growth segmentation or localized multi-scale object oriented segmentation is applied to extract small and simple rectilinear rooftops from its background; to delineate the precise position of complex rooftop, the pose clustering is applied for building locating, and model matching techniques based on node graph search is used for finding the correct building rooftop shape. Integration of these two methods makes extraction of buildings from simple rectangle rooftop to complicated building more practical. Preliminary experimental results on QuickBird imagery show that the proposed method can successfully extract about 75% of the regular building rooftops.
Efficient Blood-Brain Barrier Opening in Primates with Neuronavigation-Guided Ultrasound and Real-Time Acoustic Mapping (2018)

Brain diseases including neurological disorders and tumors remain under treated due to the challenge to access the brain, and blood-brain barrier (BBB) restricting drug delivery which, also profoundly limits the development of pharmacological treatment. Focused ultrasound (FUS) with microbubbles is the sole method to open the BBB noninvasively, locally, and transiently and facilitate drug delivery, while translation to the clinic is challenging due to long procedure, targeting limitations, or invasiveness of current systems. In order to provide rapid, flexible yet precise applications, we have designed a noninvasive FUS and monitoring system with the protocol tested in monkeys (from in silico preplanning and simulation, real-time targeting and acoustic mapping, to post-treatment assessment). With a short procedure (30 min) similar to current clinical imaging duration or radiation therapy, the achieved targeting (both cerebral cortex and subcortical structures) and monitoring accuracy was close to the predicted 2-mm lower limit. This system would enable rapid clinical transcranial FUS applications outside of the MRI system without a stereotactic frame, thereby benefiting patients especially in the elderly population.
Synthese, Struktur und photophysikalische Eigenschaften von polyarylierten Imidazolen und Oxazolen (1997)

Synthesis, Structure, and Photophysical Properties of Polyarylated Imidazoles and Oxazoles 23 tetraphenylimidazoles 1,2 and 11 triphenyloxazoles 4,5 with amino, nitro, methoxy, hydroxy, or halogeno substituents chiefly in the para position were prepared. The absorption and fluorescence emission properties were investigated in ethanolic solution. The effects of the substituents in 1,2 on the spectral shifts show that the arrangement of the phenyl rings in 1 position is not coplanar in relation to the heterocycle whereas the phenyl rings in 2 position are more coplanar. The spectral changes of compound 2a in solvents of various polarity (dielectric constants 2,02–47,24) are almost negligible. The Stokes shift is moderately increased. A remarkable increase in the fluorescence quantum yield is observed by chlorine substitution in phenyl ring 2.
Fiber-grating transmission filters for use in an all-fiber demultiplexer (1994)

Fiber phase gratings written by two-beam interference of a UV laser source1 are effective wavelength-selective reflectors and as such are particularly well suited to applications such as fiber lasers. However, there is much need for low-loss fiber transmission filters. Very-narrow-bandwidth fiber-grating Fabry– Perot transmission filters have been demonstrated.2 However, these are not suitable for applications requiring wide pass- bands.
Neutral proteases capable of proteoglycan digesting activity in osteoarthritic and normal human articular cartilage (1984)

Proteases have been postulated to account for the progressive disappearance of matrix proteoglycans in osteoarthritic (OA) cartilage. The digestion of endogenous proteoglycans by neutral proteases in human OA cartilage homogenates has been measured and compared with that of normal age-matched controls. Cartilage was obtained from 16 patients at the time of knee arthroplasty and from 7 accident victims. Tissue blocks were cut from the tibial plateau; part was used for histologic grading of the severity of OA and part was homogenized for the quantification of neutral metallo- and serine protease activities, based on the release of digested products from endogenous proteoglycans. Total metalloprotease activity (latent plus active forms) was elevated 3- to 10-fold in all diseased cartilage. This elevation was already significant in mild disease, but was greatest in samples of moderate to severe disease. The active form of the enzyme was highest at the center of erosions and decreased in the margins of the plateau. The digestion of proteoglycans, as distinct from their mere release from the tissue, was demonstrated by chromatography on Sepharose-CL2B and by large pore electrophoresis. Serine protease activity on proteoglycans was much lower than that of metalloprotease. The mean activity was highest in mild disease and declined in the severe disease samples, but the difference between these 2 groups and the controls was not statistically significant. The results of this study are consistent with the hypothesis that the neutral metalloproteases of cartilage are involved in the degradation of proteoglycans in osteoarthritis.
Vibrio choleraeO139 Conjugate Vaccines: Synthesis and Immunogenicity ofV. choleraeO139 Capsular Polysaccharide Conjugates with Recombinant Diphtheria Toxin Mutant in Mice (2000)

Epidemiologic and experimental data provide evidence that a critical level of serum immunoglobulin G (IgG) antibodies to the surface polysaccharide of Vibrio cholerae O1 (lipopolysaccharide) and of Vibrio cholerae O139 (capsular polysaccharide [CPS]) is associated with immunity to the homologous pathogen. The immunogenicity of polysaccharides, especially in infants, may be enhanced by their covalent attachment to proteins (conjugates). Two synthetic schemes, involving 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP) as activating agents, were adapted to prepare four conjugates of V. cholerae O139 CPS with the recombinant diphtheria toxin mutant, CRMH21G. Adipic acid dihydrazide was used as a linker. When injected subcutaneously into young outbred mice by a clinically relevant dose and schedule, these conjugates elicited serum CPS antibodies of the IgG and IgM classes with vibriocidal activity to strains of capsulated V. cholerae O139. Treatment of these sera with 2-mercaptoethanol (2-ME) reduced, but did not eliminate, their vibriocidal activity. These results indicate that the conjugates elicited IgG with vibriocidal activity. Conjugates also elicited high levels of serum diphtheria toxin IgG. Convalescent sera from 20 cholera patients infected with V. cholerae O139 had vibriocidal titers ranging from 100 to 3,200: absorption with the CPS reduced the vibriocidal titer of all sera to < or =50. Treatment with 2-ME reduced the titers of 17 of 20 patients to < or =50. These data show that, like infection with V. cholerae O1, infection with V. cholerae O139 induces vibriocidal antibodies specific to the surface polysaccharide of this bacterium (CPS) that are mostly of IgM class. Based on these data, clinical trials with the V. cholerae O139 CPS conjugates with recombinant diphtheria toxin are planned.
Endocrine Therapy of Breast Cancer (2005)

Abstract : A recent controversy in the treatment of estrogen receptor positive (ER+) breast cancers is whether an aromatase inhibitor, e.g., letrozole (LET) or TAM should be given as first line endocrine therapy. Unfortunately, response rates are lower, and response durations are shorter, on crossover than when these agents are given as first line therapies, e.g., ~40% of tumors show crossresistance to TAM or an aromatase inhibitor on crossover. Only 50% of ER+ tumors respond to endocrine therapy. Currently, we fail to predict endocrine responsiveness in about 66% of ER+/PgR- (progesterone receptor), 55% of ER-/PgR+, and 25% of ER+/PgR+ tumors. In this new Clinical Translational Research Award, we hypothesize that our analytical methods can extract expression profiles of breast tumors that define their responsiveness (sensitive vs. resistant) to endocrine therapy. These profiles, when combined with known predictive/prognostic factors, will support neural network and biostatistical classifiers or committee machines that predict each tumor's endocrine responsiveness. Our objectives are to array breast cancer cases, build classifiers of endocrine responsiveness (using microarray data), and validate these classifiers in independent data sets. In the long term, we will design custom arrays for use in clinical practice. Genes will be further studied using cellular and molecular methods, and their role as therapeutic targets explored.
Blood-Brain Barrier Disruption By Low-Frequency Ultrasound (2006)

Abnormal permeability of the human blood-brain barrier can be induced by wide-field low-frequency insonation. The observed excessive bleeding rate with low-frequency sonothrombolysis might thus be attributable to primary blood-brain barrier disruption by ultrasound.
Evaluation of pimobendan in dogs with cardiomegaly caused by preclinical mitral valve disease (2011)

Epidemiological and modelling studies suggest that elimination of Onchocerca volvulus transmission (EoT) throughout Africa may not be achievable with annual mass drug administration (MDA) of ivermectin alone, particularly in areas of high endemicity and vector density. Single-dose Phase II and III clinical trials demonstrated moxidectin's superiority over ivermectin for prolonged clearance of O. volvulus microfilariae. We used the stochastic, individual-based EPIONCHO-IBM model to compare the probabilities of reaching EoT between ivermectin and moxidectin MDA for a range of endemicity levels (30 to 70% baseline microfilarial prevalence), treatment frequencies (annual and biannual) and therapeutic coverage/adherence values (65 and 80% of total population, with, respectively, 5 and 1% of systematic non-adherence). EPIONCHO-IBM's projections indicate that biannual (six-monthly) moxidectin MDA can reduce by half the number of years necessary to achieve EoT in mesoendemic areas and might be the only strategy that can achieve EoT in hyperendemic areas. Data needed to improve modelling projections include (i) the effect of repeated annual
Surface crosslinking of polyethylene using a hydrogen glow discharge (1972)

Abstract Linear high‐density polyethylene is crosslinked by exposing it to a hydrogen glow discharge and alternatively by exposing it to a low‐pressure Hg–A ultraviolet lamp in a dry nitrogen atmosphere. For the UV lamp case, the crosslinked gel is measured as a function of the radiation dose. For the plasma case, the crosslinked gel is measured as a function of the exposure time. The two gelation curves are alternatively compared to an exponentially attenuated light theory and a diffusion theory. Excellent agreement exists between the measured gel‐versus‐dose curve and the theoretical curve based on the light theory for a monochromatic light beam at 1849 Å. The gelation curve for the hydrogen glow discharge case can be explained using the identical theory but applied to a spectrum of light covering the range from 1200 Å to 1900 Å. The different curves can be explained in terms of the different spectra. Energy transfer between the plasma and the polymer due to excited atoms, and/or charged particles, is not required to account for the different gel curves.
Tension-Free Inguinal Hernia Repair: The Design of a Trial to Compare Open and Laparoscopic Surgical Techniques (2003)

We report successful recruitment into a large multicenter trial comparing open and laparoscopic hernia repair. When followup is complete, this study will provide data regarding both clinical (recurrence rates) and patient-centered outcomes.
Hepatic Lipase as a Focal Point for the Development and Treatment of Coronary Artery Disease (2001)

Recent epidemiological evidence suggests that although lowering low-density lipoprotein (LDL) cholesterol is important in decreasing cardiovascular disease morbidity and mortality, it accounts only for part of the coronary artery disease (CAD) improvement with lipid-lowering therapy. In the last decade, it has become evident that the atherogenicity of LDL particles is associated not only with their plasma levels, but also with their size and density. The presence of small, dense LDL particles is associated with a three fold increase in CAD risk. Hepatic lipase (HL), a key enzyme in the formation of small, dense LDL particles, modulates their phospholipid and triglyceride contents. The higher the HL activity, the smaller, denser, and more atherogenic the resulting lipoprotein particle. It is, therefore, plausible to hypothesize that at least part of the CAD benefits observed in the recent CAD-prevention pharmacological trials, which are not accounted for by the decrease in LDL-C (LDL-cholesterol), might be explained by a pharmacological effect on LDL size and density, possibly mediated by changes in hepatic lipase activity. By studying patients with dyslipidemia and CAD, we have been able to provide strong evidence that regression of coronary atherosclerosis results from at least two independent effects of lipid-lowering therapy on lipoprotein metabolism: the well known one that leads to changes in LDL-C and apo B levels, and a new pathway of HL-mediated improvement in LDL buoyancy. Finally, HL activity and LDL density appear to be significantly affected by the presence of a common C-->T substitution at position -514 with respect to the transcription start site of the HL gene, raising the possibility that the -514 C-->T polymorphism may significantly contribute to differences in individual CAD response to lipid-lowering treatment, as seen in the recent major primary and secondary CAD-prevention clinical trials.
Identification of d-Proline Reductase fromClostridium sticklandiias a Selenoenzyme and Indications for a Catalytically Active Pyruvoyl Group Derived from a Cysteine Residue by Cleavage of a Proprotein (1999)

Highly active D-proline reductase was obtained from Clostridium sticklandii by a modified purification scheme. The cytoplasmic enzyme had a molecular mass of about 870 kDa and was composed of three subunits with molecular masses of 23, 26, and 45 kDa. The 23-kDa subunit contained a carbonyl group at its N terminus, which could either be labeled with fluorescein thiosemicarbazide or removed by o-phenylenediamine; thus, N-terminal sequencing became feasible for this subunit. L-[14C]proline was covalently bound to the 23-kDa subunit if proline racemase and NaBH4 were added. Selenocysteine was detected in the 26-kDa subunit, which correlated with an observed selenium content of 10.6 g-atoms in D-proline reductase. No other non-proteinaceous cofactor was identified in the enzyme. A 4.8-kilobase pair (kb) EcoRI fragment was isolated and sequenced containing the two genes prdA and prdB. prdA coding for a 68-kDa protein was most likely translated as a proprotein that was posttranslationally cleaved at a threonine-cysteine site to give the 45-kDa subunit and most probably a pyruvoyl-containing 23-kDa subunit. The gene prdB encoded the 26-kDa subunit and contained an in frame UGA codon for selenocysteine insertion. prdA and prdB were transcribed together on a transcript of 4.5 kb; prdB was additionally transcribed as indicated by a 0.8-kb mRNA species.
Tracking anonymous peer-to-peer VoIP calls on the internet (2005)

Peer-to-peer VoIP calls are becoming increasingly popular due to their advantages in cost and convenience. When these calls are encrypted from end to end and anonymized by low latency anonymizing network, they are considered by many people to be both secure and anonymous.In this paper, we present a watermark technique that could be used for effectively identifying and correlating encrypted, peer-to-peer VoIP calls even if they are anonymized by low latency anonymizing networks. This result is in contrast to many people's perception. The key idea is to embed a unique watermark into the encrypted VoIP flow by slightly adjusting the timing of selected packets. Our analysis shows that it only takes several milliseconds time adjustment to make normal VoIP flows highly unique and the embedded watermark could be preserved across the low latency anonymizing network if appropriate redundancy is applied. Our analytical results are backed up by the real-time experiments performed on leading peer-to-peer VoIP client and on a commercially deployed anonymizing network. Our results demonstrate that (1) tracking anonymous peer-to-peer VoIP calls on the Internet is feasible and (2) low latency anonymizing networks are susceptible to timing attacks.
Endothelial Replacement and Angiogenesis in Arteriosclerotic Lesions of Allografts Are Contributed by Circulating Progenitor Cells (2003)

We provide strong evidence that endothelial cells of neointimal lesions in allografts are derived from circulating progenitor cells and that bone marrow-derived progenitors are responsible for angiogenesis of the allograft, that is, the formation of microvessels in transplant arteriosclerosis.
The V(D)J recombination signal sequence and χB binding protein Rc binds DNA as dimers and forms multimeric structures with its DNA ligands (1994)

The murine DNA binding protein Rc binds to the heptamer motif of the V(D)J recombination signal sequences and to the kappa B motif of the immunoglobulin enhancer. Bacterial fusion proteins for Rc and DNA ligands of Rc form multiple protein-DNA complexes in electrophoretic mobility shift assays (EMSA). Large complexes formation is favored by an increased Rc concentration. In order to determine the architecture of these complexes, the apparent molecular weights of the protein-DNA complexes were first determined by their gel mobilities. The data suggest that Rc binds to its DNA ligands as dimers, tetramers, and multiples of tetramers. The inference that Rc binds DNA as dimers was substantiated by the formation of chimeric complexes when two electrophoretically distinguishable Rc proteins were employed in EMSA. Methylation interference experiments show that there are no contiguous protein binding sites evident in the DNA of the larger complexes. Apparently, multimerization occurs via protein-protein interactions. Such interaction was demonstrated by the formation of Rc dimers and tetramers in a chemical crosslinking experiment. Significantly, the multimerization of DNA-bound Rc could be involved in bringing the variable region gene segments together for the somatic V(D)J recombination.
Genomic Structure and Transcriptional Regulation of the Human Growth Hormone Secretagogue Receptor1 (2001)

Synthetic GH secretagogues stimulate GH release through binding to a recently cloned specific GH secretagogue receptor (GHS-R). The endogenous ligand of this receptor may be part of a new endocrine pathway controlling GH secretion. Two different receptor variants, type 1a and 1b, have been described that differ in their 3'-terminal amino acids. We investigated the genomic structure and transcriptional regulation of the human GHS-R. An 18-kb genomic clone including sequences encoding for the two GHS-R variants was isolated. Sequencing revealed that the two variants originate from specific RNA processing of a single gene that spans approximately 4.1 kb. The transcription start site was defined by 5'-inverse PCR analysis at position -227. RT-PCR analysis points to differential transcriptional initiation and processing. Type 1a is encoded by two exons; 2152 bp of intronic sequence are removed by splicing at position 796/797 relative to the translation start site. Type 1b is encoded by a single exon. A putative polyadenylation signal consensus motif was identified at position +4118; 2.7 kb of the 5'-flanking region were sequenced, and putative transcription factor binding sites were identified. Transcriptional regulation was investigated by transient transfections using promoter fragments ranging in size from 168-1745 bp; 1745 bp of the GHS-R promoter directed significant levels of luciferase expression in GH(4) rat pituitary cells, whereas no activity was detected in monkey kidney COS-7 cells, human endometrium Skut-1B cells, mouse hypothalamic LHRH neuronal GT1-7 cells, or mouse corticotroph pituitary AtT20 cells. A minimal 309-bp promoter allowed pituitary-specific expression. Its activity in COS-7 cells was enhanced by cotransfection of the pituitary-specific transcription factor Pit-1. We did not find any regulation of the GHS-R promoter by forskolin, somatostatin, insulin-like growth factor I, or 12-O-tetraphorbol 12-myristate 13-acetate. Thyroid hormone and estrogen lead to a significant stimulation; glucocorticoids lead to a significant inhibition. Further mapping suggests a thyroid hormone-responsive element, an estrogen-responsive element, and a glucocorticoid-responsive element located between -309 and the translation start codon. These studies demonstrate the nature of the human GHS-R gene and identify its 5'-flanking region. Furthermore, pituitary-specific activity of the promoter and regulation by various hormones are demonstrated.
A Self-Deleting AAV-CRISPR System for In Vivo Genome Editing (2018)

Adeno-associated viral (AAV) vectors packaging the CRISPR-Cas9 system (AAV-CRISPR) can efficiently modify disease-relevant genes in somatic tissues with high efficiency. AAV vectors are a preferred delivery vehicle for tissue-directed gene therapy because of their ability to achieve sustained expression from largely non-integrating episomal genomes. However, for genome editizng applications, permanent expression of non-human proteins such as the bacterially derived Cas9 nuclease is undesirable. Methods are needed to achieve efficient genome editing <i>in vivo</i>, with controlled transient expression of CRISPR-Cas9. Here, we report a self-deleting AAV-CRISPR system that introduces insertion and deletion mutations into AAV episomes. We demonstrate that this system dramatically reduces the level of <i>Staphylococcus aureus</i> Cas9 protein, often greater than 79%, while achieving high rates of on-target editing in the liver. Off-target mutagenesis was not observed for the self-deleting Cas9 guide RNA at any of the predicted potential off-target sites examined. This system is efficient and versatile, as demonstrated by robust knockdown of liver-expressed proteins <i>in vivo</i>. This self-deleting AAV-CRISPR system is an important proof of concept that will help enable translation of liver-directed genome editing in humans.