gebhart/patrepeval huggingface dataset:
Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage (2019)

Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; <i>n</i> = 109) sampled in ninteen countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172-3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
Intermediates for the Synthesis of 4-Substituted Proline Derivatives (2010)

chemoenzymatic synthesis of a series of 2-hydroxy-5-nitro-4-substituted esters is described that uses two biotransformations in a single-pot process in which a kinetic resolution/reduction occurs. The products are valuable intermediates for the preparation of 4-substituted prolines and 5-substituted 3-hydroxypiperidinones as illustrated by the preparation of (2R,4R)-4-methylproline and (3S,5R)-3-hydroxy-5-methylpiperidinone.
Herstellung von Boranaloga von Enaminen über Hydroaminierung einer Bor‐Bor‐Dreifachbindung (2020)

Abstract Ein durch N‐heterocyclische Carbene stabilisiertes Diborin geht bei Umsetzung mit primären Aminen schnelle, katalysatorfreie Hydroaminierungsreaktionen in hohen Ausbeuten ein. Die erhaltenen 1‐Amino‐2‐hydrodiborene können als Boranaloga von Enaminen beschrieben werden. Die elektronischen Eigenschaften der organischen Substituenten der Stickstoffatome beeinflussen die Struktur und die Folgereaktivität der Diborene. Mit elektronenreichen Anilinderivaten besteht die Möglichkeit einer zweiten Hydroaminierung, wodurch 1,1‐Diamino‐2,2‐dihydrodiborane gebildet werden. Der elektronische Einfluss des Alkylsubsituenten von Isopropylamin führt nach Bildung des Diborens zu einer unerwarteten borvermittelten intramolekularen N‐Dearylierung einer Carbeneinheit.
Wide-field retinal optical coherence tomography with wavefront sensorless adaptive optics for enhanced imaging of targeted regions (2016)

The peripheral retina of the human eye offers a unique opportunity for assessment and monitoring of ocular diseases. We have developed a novel wide-field (>70°) optical coherence tomography system (WF-OCT) equipped with wavefront sensorless adaptive optics (WSAO) for enhancing the visualization of smaller (<25°) targeted regions in the peripheral retina. We iterated the WSAO algorithm at the speed of individual OCT B-scans (~20 ms) by using raw spectral interferograms to calculate the optimization metric. Our WSAO approach with a 3 mm beam diameter permitted primarily low- but also high- order peripheral wavefront correction in less than 10 seconds. In preliminary imaging studies in five normal human subjects, we quantified statistically significant changes with WSAO correction, corresponding to a 10.4% improvement in average pixel brightness (signal) and 7.0% improvement in high frequency content (resolution) when visualizing 1 mm (~3.5°) B-scans of the peripheral (>23°) retina. We demonstrated the ability of our WF-OCT system to acquire non wavefront-corrected wide-field images rapidly, which could then be used to locate regions of interest, zoom into targeted features, and visualize the same region at different time points. A pilot clinical study was conducted on seven healthy volunteers and two subjects with prodromal Alzheimer's disease which illustrated the capability to image Drusen-like pathologies as far as 32.5° from the fovea in un-averaged volume scans. This work suggests that the proposed combination of WF-OCT and WSAO may find applications in the diagnosis and treatment of ocular, and potentially neurodegenerative, diseases of the peripheral retina, including diabetes and Alzheimer's disease.
A Genetic Analysis of Carbon‐Nanotube‐Binding Proteins (2008)

Udgivelsesdato: 18. Mar.
ChemInform Abstract: Self‐Assembly of Nanostructures from Inorganic Building Blocks (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
High-performance 980-nm emission wavelength InGaAs/AlGaAs/GaAs laser diodes (2000)

This paper present the fabrication and mirrors passivation process of InGaAs/AlGaAs/GaAs narrow stripe 980 nm emission wavelength laser diodes. After mesa-stripe definition and Au-contact deposition procedures, a procedure of in-vacuum cleaving and in-situ passivation with (lambda) /2-thick ZnSe layers was performed. 960 micrometers and 500 micrometers length laser diodes bars was fabricated as a result. Antireflection-high reflectivity coating were formed on the bars facets. Laser diodes were soldered p-junction-side down on copper submounts. The room temperature CW threshold current value of 20 mA and CW maximum output power of 440 mW at 760 mA pumping current were obtained. The far-field emission pattern of laser diodes is lateral single mode in large range of output powers. These laser diodes were used for laser diode module fabrication. In this module the laser diodes was coupled with tapered single mode 9 micrometers /125 micrometers optical fiber with a fused microlens at the end. CW output optical power of 40 mW from the fiber was obtained at 240 mA operating current of the laser diode module.
A quantitative investigation of fucosylated serum glycoproteins with application to esophageal adenocarcinoma (2010)

Although glycoproteomic studies provide unique opportunities for cancer research, it has been necessary to develop specific methods for analysis of oncologically interesting glycoproteins. We describe a general, multimethodological approach for quantitative glycoproteomic analysis of fucosylated glycoproteins in human blood serum. A total of 136 putative fucosylated glycoproteins were identified with very high confidence in three clinically relevant sample pools (N=5 for each), with a mean CV of 3.1% observed for replicate analyses. Two samples were collected from subjects diagnosed with esophagus disease states, high-grade dysplasia plus esophageal adenocarcinoma, while the third sample was representative of a disease-free condition. Some glycoproteins, observed to be significantly upregulated in esophageal adenocarcinoma, i.e. more than twofold higher than in the disease-free condition, are briefly discussed. Further investigation will be necessary to validate these findings; however, the method itself is demonstrated to be an effective tool for quantitative glycoproteomics of clinical samples.
[Antiplasmin drugs and factor XIII concentrates in the treatment of a patient with acute promyelocytic leukemia (M3)]. (1989)

A female patient what M3 was seen to incur marked hemorrhagic diathesis during therapy. Heparin infusion was performed to inhibit disseminated intravascular coagulation (DIC). However, oozing from the puncture site of the r-subclavian vein was observed. Her data on coagulation were as follows: AT-3 greater than 100%, fibrinogen 69.0 mg, XIII less than 40%, FPA 2.9 ng/ml and FDP-D dimer 256 ng/ml. The alpha-2-plasmin inhibitor (alpha 2-PI) was 44% and FDP 160 microgram/ml. These results suggested DIC with activated fibrinolysis. Thus, epsilon aminocaproic acid in conjunction with heparin, fibrinogen, and concentrated XIII was administered. The abnormal bleeding improved with an increase of alpha 2-PI and XIII. This clinical response indicated that an activated fibrinolysis and a decreased XIII might have been responsible for provoking the bleeding of the patient.
Ion beam thinning and polishing of YBa2Cu3O7 films (1989)

Successive ion beam milling at grazing angles of a 2400-Å-thick, c-axis-oriented YBa2Cu3O7 film is shown to give smooth films which superconduct at thicknesses on the order of tens of angstroms. The thinning and polishing process is characterized at successive milling stages using resistance transitions, x-ray analysis, scanning electron microscopy, and Rutherford backscattering and channeling analysis of composition and surface quality. As thinning proceeds, scanning electron microscopy and diffraction features associated with a-axis texture are removed and crystalline quality, as measured by x rays and channeling, markedly improves.
Demonstration of a Negative-Refractive-Index Lens Imaging System (2022)

An imaging system comprising a planar negative-refractive-index lens and a pair of small loop antennas is described. The two loops antennas are fixed on one side of the lens, and the object is transversely scanned across the other side. One loop illuminates the object through the lens. Reflection from the object is focused by the lens onto a plane containing the other loop. This loop senses both reflected and incident fields. An image is constructed by relating transmission (S21) between the loops to the object translation. The system was demonstrated experimentally at 3 GHz and supported by theory.
Research of Urban Bus Stop Planning Based on Optimization Theory (2009)

According to the difficulty of urban bus stop planning, a method which is based on optimization theory is introduced. First, the minimum passengerspsila total traveling time model base on the shortest stop distance is adopted to calculate the optimum stop distance and determine the number of bus stops. Then, the bus stop coverage rate model is used to predict the development scale of urban bus stop. Finally, based on a comprehensive analysis of these two models, the rational development scale of urban bus stop is determined. The method has been applied in Zhanjiangpsilas public traffic planning, the experiment shows that the method is brief and easy, it has some real work significance to public traffic planning.
Report on the development of a new dental curriculum at Helsinki (2001)

A review of the dental curriculum was undertaken in Helsinki in the mid 90s. The objectives of the new curriculum were to reinforce the links between basic biomedical and dental sciences in order to give more emphasis to oral medicine and comprehensive dental care. Furthermore, the curriculum needed to promote an interdisciplinary approach and encourage students to understand dental diseases in relation to the community at large. A two-year, topic-based, preclinical curriculum, fully integrated with medical students, was started. For didactic teaching in the clinical phase, new learning entities were established to promote an inter-disciplinary approach. For the first time in Finland, objectives were formulated for attitudes and interpersonal skills. Clinical training was conducted in a comprehensive clinic, based on the team concept, where emphasis was given to proven competency instead of to the number of procedures performed. The time spent in the clinic was kept the same as previously (1440 h). Students' learning process was assessed with a portfolio. The majority of students welcomed the comprehensive care clinic, especially its team concept and treatment planning seminars. However, feedback seminars after treatment of the patient were not in favour. As part of the evaluation process, a DENTED visitation took place in Helsinki in March 1999. The results obtained in the student questionnaire were consistent with the aims of the undergraduate training and with the present patient treatment range. In conclusion, the curriculum change enabled the school to broaden the biomedical aspects by increasing the period of preclinical studies. Although the extent of these studies was greater than in the past, and meant postponement of clinical skills courses by one semester, it did not jeopardise the competency in clinical dentistry, owing to the effective integration of the clinical phase teaching.
Lymphoblastic lymphoma in children--a randomized trial comparing LSA2-L2 with the A-COP+ therapeutic regimen: a Pediatric Oncology Group Study. (1988)

From May 1979 to March 1983, 76 evaluable patients with lymphoblastic lymphoma (LBL) were treated by members of the Pediatric Oncology Group (POG). Forty-six children treated by the six-drug A-COP+ regimen (Adriamycin [doxorubicin; Adria Laboratories, Columbus, OH], vincristine, prednisone, cyclophosphamide, methotrexate, and hydrocortisone) were compared in a prospective randomized trial with 30 patients receiving the modified ten-drug LSA2-L2 (cyclosphosphamide, vincristine, methotrexate, Daunomycin [daunorubicin cerubidine; Wyeth Laboratories, Philadelphia], prednisone, cytarabine, thioguanine, asparaginase, hydroxyurea, and carmustine) regimen. After adjusting for stage (I and II v III v IV), there was no statistically significant difference (P = .19) between A-COP+ and LSA2-L2 regimens on the basis of 3-year survival and disease-free survival (62% v 72% and 53% v 58%, respectively for the two treatment regimens) but the power of analysis and thus the ability to detect a clinically meaningful difference in the outcome with the two regimens was limited by the small number of patients. Neither therapy was effective for most patients with stage IV disease, with failure occurring in six of seven children receiving A-COP+ regimen and eight of 11 patients receiving LSA2-L2. Although the LSA2-L2 regimen was more toxic during the induction of remission, the toxicity during maintenance was acceptable and similar for both treatments. CNS relapse was not a significant problem whether cranial radiation with intrathecal (IT) therapy (A-COP+) or IT therapy alone (LSA2-L2) were used. Our results confirm the overall effectiveness of the LSA2-L2 regimen in children with LBLs, especially those initially free of bone marrow or CNS involvement, but were inconclusive as to the inferiority or superiority of this regimen over the A-COP+ regimen.
Pharmacokinetics and bioavailability of doxycycline hyclate after oral administration in calves (1993)

The bioavailability and pharmacokinetics of doxycycline hyclate were determined in calves with immature rumen function. The bioavailability of doxycycline after oral administration in a milk replacer was approximately 70%. The elimination half-life of doxycycline was found to be 9.5 +/- 3.0 h. after intravenous administration, and 12.6 +/- 5.0 h. after single oral administration. Plasma concentrations were determined after repeated oral administration of doxycycline dissolved in a milk replacer, at a dose of 5 mg per kg body weight, twice daily. During the period of administration, the plasma concentrations varied between Cmin of 1.0 +/- 0.19 mg/L and Cmax of 2.3 +/- 0.19 mg/L.
Microbial-assisted remediation of creosote- and pentachlorophenol-treated wood products (1996)

A recycling process designed to recover wood fiber from discarded utility poles and cross ties was tested. Laboratory and field studies were conducted using a combined physical, chemical and microbiological protocol designed for the removal of creosote and pentachlorophenol wood preservatives from wood fiber. Woodchips produced in an industrial type wood chipper were batch extracted in methanol. The extractions successfully removed more than 95% of eight major creosote compounds contained within the woodchips. An initial combined concentration of 29 262 ppm during the extraction phase was reduced to 95 ppm in the laboratory study and to 1364 ppm in the field study. Biopolishing with a microbial consortium containing adapted strains from the generaPseudomonas, Flavobacterium andAcinetobacter further reduced the preservative concentration to 8 ppm and 200 ppm, respectively, with anthracene being the most recalcitrant compound in both studies. Pentachlorophenol-treated wood with an initial concentration of 1190 ppm, when subjected to the recycling process, yielded end product wood containing less than 2 ppm of the preservative. The solvent/preservative mixture (miscella) produced during the extraction process yielded a pure methanol fraction and a still bottom mixture when subjected to flash distillation. Fractional (vacuum) distillation of the still bottom mixture produced methanol, creosote, pentachlorophenol, and coal tar fractions.
Inhibition of G protein-coupled receptor signaling by expression of cytoplasmic domains of the receptor. (1994)

The third intracellular domain (3i) of G protein-coupled receptors plays a major role in the activation of G proteins. Alterations in this region of the receptor can affect receptor/G protein coupling efficiency and specificity. We recently reported (Luttrell, L. M., Cotecchia, S., Ostrowski, J., Kendall, H., Lefkowitz, R.J. (1993) Science 259, 1453-1457) that coexpression of the 3i domain of the alpha 1B adrenergic receptor (AR) (alpha 1B3i) specifically inhibited alpha 1BAR-mediated inositol phosphate production, with no effect on D1A dopamine receptor (D1ADR)-mediated cAMP production. Similarly, expression of the 3i domain of D1ADR (D1A3i) inhibited D1ADR-mediated cAMP production but did not affect alpha 1BAR-mediated inositol phosphate accumulation. This suggests that peptides derived from a G protein-coupled receptor might serve as antagonists of receptor/G protein interactions. The present studies were performed to test the generality as well as the specificity of this phenomenon. The effect of expression of the second intracellular domain (2i), the 3i domain, and the fourth intracellular domain (4i) of alpha 1BAR on second messenger generation mediated by the alpha 1BAR, the M1 muscarinic cholinergic receptor (M1AChR), and the D1ADR was examined. Although the alpha 1B2i domain had no effect on receptor/G protein coupling for any receptor tested, the alpha 1B3i domain inhibited signaling mediated by alpha 1BAR and M1AChR but not by D1ADR, while the alpha 1B4i domain inhibited signaling mediated by each of the receptors. To investigate the generality of 3i domain-induced inhibition of receptor activity further, the 3i domains of two Gq-coupled receptors (alpha 1BAR and M1AChR) and two Gi-coupled receptors (alpha 2AAR and M2AChR) were tested for effects on the second messenger generation mediated by each of the four receptors. In each case, the homologous 3i domain caused significant inhibition (40-60%), while the 3i domain of the receptor coupled to the same G protein also decreased receptor/G protein coupling. In contrast, receptor/G protein coupling appeared unaffected by expression of 3i domains derived from receptors coupled to different G proteins. The alpha 1B3i domain-provoked inhibition of homologous receptor signaling was surmountable at high receptor density, and assays using a phorbol response element/reporter gene construct detected a weak enhancement of basal second messenger generation in cells expressing the alpha 1B3i domain alone.(ABSTRACT TRUNCATED AT 400 WORDS)
A Computed Tomographic Guide to the Identification of Cerebral Vascular Territories (1983)

This article presents a system of human brain templates, depicting territories of cerebrovascular supply and cortical cytoarchitectonic markings. The templates may be used as a guide to localization of abnormal images in standard computed tomographic cuts.
Allergic Fungal Sinusitis in the Pediatric Population (1996)

The treatment and prognosis of pediatric AFS are similar to those of adult AFS. However, systemic corticosteroids should be weaned aggressively in children to minimize complications, particularly long-term growth retardation.
Piano music transcription modeling note temporal evolution (2015)

Automatic music transcription (AMT) is the process of converting an acoustic musical signal into a symbolic musical representation such as a MIDI piano roll, which contains the pitches, the onsets and offsets of the notes and, possibly, their dynamic and source (i.e., instrument). Existing algorithms for AMT commonly identify pitches and their saliences in each frame and then form notes in a post-processing stage, which applies a combination of thresholding, pruning and smoothing operations. Very few existing methods consider the note temporal evolution over multiple frames during the pitch identification stage. In this work we propose a note-based spectrogram factorization method that uses the entire temporal evolution of piano notes as a template dictionary. The method uses an artificial neural network to detect note onsets from the audio spectral flux. Next, it estimates the notes present in each audio segment between two successive onsets with a greedy search algorithm. Finally, the spectrogram of each segment is factorized using a discrete combination of note templates comprised of full note spectrograms of individual piano notes sampled at different dynamic levels. We also propose a new psychoacoustically informed measure for spectrogram similarity.
Suicidal disorders: A nosological entity per se? (2005)

An extensive body of data has repeatedly shown in the past decades that suicidal behaviors are associated with several external validators such as low serotonergic activity in body fluids and in brains of suicide victims, genetic transmission of suicide risk independently of transmission of associated major psychiatric disorders, and more recently association with several serotonin-related genes. Despite these concordant findings, suicidal behaviors are still not considered as a nosological entity per se in standardized classification. The aim of this study is to review the existing literature establishing the validity of this entity through clinical, genetic, biochemical, and therapeutic arguments all leading to the need to recognizing suicidal behavior as an independent and possibly dimensional clinical entity.
Censoring of Autoreactive B Cell Development by the Pre-B Cell Receptor (2008)

Antibody diversity occurs randomly as B cells recombine their immunoglobulin (Ig) heavy- and light-chain genes during development. This process inevitably generates reactivity against self structures, and several mechanisms prevent the development of autoreactive B cells. We report here a role for the pre-B cell receptor, composed of Ig heavy and surrogate light chains, in the negative selection of cells expressing Ig heavy chains with the potential to generate autoantibodies. Surrogate light-chain-deficient (SLC-/-) mice harbored elevated levels of antinuclear antibodies (ANAs) in their serum and showed evidence of escape of pre-B cells expressing prototypic autoantibody heavy chains from negative selection, leading to mature autoantibody secreting CD21-CD23- B cells in the periphery. Thus, the pre-B cell receptor appears to censor the development of certain autoantibody-secreting cells and may represent an important factor in multifactorial autoimmune diseases.