gebhart/patrepeval huggingface dataset:
Resistance profiles of emtricitabine and lamivudine in tenofovir-containing regimens (2012)

Emtricitabine and lamivudine showed differing resistance profiles when administered in combination with tenofovir disproxil fumarate and either efavirenz or a ritonavir-boosted PI. The prevalence of the M184V/I resistance mutation was significantly lower in patients who received emtricitabine and tenofovir disoproxil fumarate than in those who received lamivudine and tenofovir disoproxil fumarate.
Continuous live imaging of adult neural stem cell division and lineage progression in vitro (2011)

Little is known about the intrinsic specification of adult neural stem cells (NSCs) and to what extent they depend on their local niche. To observe adult NSC division and lineage progression independent of their niche, we isolated cells from the adult mouse subependymal zone (SEZ) and cultured them at low density without growth factors. We demonstrate here that SEZ cells in this culture system are primarily neurogenic and that adult NSCs progress through stereotypic lineage trees consisting of asymmetric stem cell divisions, symmetric transit-amplifying divisions and final symmetric neurogenic divisions. Stem cells, identified by their astro/radial glial identity and their slow-dividing nature, were observed to generate asymmetrically and fast-dividing cells that maintained an astro/radial glia identity. These, in turn, gave rise to symmetrically and fast-dividing cells that lost glial hallmarks, but had not yet acquired neuronal features. The number of amplifying divisions was limited to a maximum of five in this system. Moreover, we found that cell growth correlated with the number of subsequent divisions of SEZ cells, with slow-dividing astro/radial glia exhibiting the most substantial growth prior to division. The fact that in the absence both of exogenously supplied growth factors and of signals provided by the local niche neurogenic lineage progression takes place in such stereotypic fashion, suggests that lineage progression is, to a significant degree, cell intrinsic or pre-programmed at the beginning of the lineage.
The Effects of Nested Primer Binding Sites on the Reproducibility of PCR: Mathematical Modeling and Computer Simulation Studies (1996)

The polymerase chain reaction (PCR) has become an indispensable tool in modern biological research. Although the application of PCR is a standard routine, we widely lack a theoretical understanding of the dynamic processes involved, especially with respect to the amplification of nonreproducible and/or unexpected amplification products. For one potential source of uncertainty, the presence of nested primer binding sites within an amplifyable DNA locus, we consider a simple stochastic model for the dynamics of PCR amplification of competing products. For commonly used thermostable DNA polymerases lacking a 5'-3'-exonuclease activity, we predict the relative amplification frequencies of competing PCR products dependent on the primer binding probability, the number of PCR cycles, and the number of initial DNA template molecules. At low primer binding probabilities and low numbers of initial DNA template molecules and PCR cycles, we expect the amplification of two products. At high primer binding probabilities and/or high copy numbers of initial template molecules only one main amplification product is predicted at increasing cycle numbers. Furthermore, by means of computer simulation studies we quantify the stochastic variation for the amplification frequencies of competing products.
Efficient near-duplicate detection and sub-image retrieval (2004)

We introduce a system for near-duplicate detection and sub-image retrieval. Such a system is useful for finding copyright violations and detecting forged images. We define near-duplicates as images altered with common transformations such as changing contrast, saturation, scaling, cropping, framing, etc. Our system builds a parts-based representation of images using distinctive local descriptors which give high quality matches even under severe transformations. To cope with the large number of features extracted from the images, we employ locality-sensitive hashing to index the local descriptors. This allows us to make approximate similarity queries that only examine a small fraction of the database. Although locality-sensitive hashing has excellent theoretical performance properties, a standard implementation would still be unacceptably slow for this application. We show that, by optimizing layout and access to the index data on disk, we can efficiently query indices containing millions of keypoints. Our system achieves nearperfect accuracy (100 % precision at 99.85 % recall) on the tests presented in Meng et al. [16], and consistently strong results on our own, significantly more challenging experiments. Query times are interactive even for collections of thousands of images.
<title>Embedded nano-optic media for near-field high-density optical data storage: modeling, fabrication, and performance</title> (2002)

The promise of near-field (NF) optics to increase the density in optical data storage, whether solid immersion lenses (SILs), apertures, or their variants, has not yet been fulfilled, largely because of the difficulties with the head-media interface at near-field dimensions, especially if a design goal is removable media. We introduce a new approach to NF optical storage, in which the near-field elements, in the form of cylindrical NF nano-optics (nOptics), are integral with the media. Combining the advantages of near- and far-field optical data storage, we obtain double the track density of DVD in removable rewritable phase change media. Potential for in-track density increase is also demonstrated. We briefly report on the modeling, manufacture, and performance of NF nOptic media.
Antipeptide antibody to the insulin-like growth factor-I receptor sequence 1232-1246 inhibits the receptor kinase activity. (1992)

To approach the question of why insulin-like growth factor-I (IGF-I) and insulin have different physiological actions, we developed antibodies directed against cytoplasmic regions of the IGF-I receptor exhibiting a low degree of homology with the corresponding sequences of the insulin receptor. We found that an antipeptide antibody directed against the beta-subunit carboxyl-terminal sequence (1232-1246) of the IGF-I receptor significantly reduced the in vitro receptor autophosphorylation. The ability of the synthetic peptide corresponding to the IGF-I receptor sequence 1232-1246 to abolish this inhibitory effect reflects the specific nature of the antibody interaction with the targeted domain in the receptor. Antipeptide antibody to IGF-I receptor sequence 1232-1246 also decreased receptor phosphorylation activity toward the exogenous substrate poly(Glu/Tyr). The reduction in poly(Glu/Tyr) phosphorylation was seen even when the antibody was incubated with a receptor previously activated and phosphorylated. Therefore, the inhibitory action on substrate phosphorylation is likely to be unrelated to the antibody reduction of receptor autophosphorylation but rather results from a global decrease in receptor enzymatic activity. The effect of the antipeptide antibody on receptor tyrosine kinase cannot be accounted for by a lowering of the receptor Km for ATP or of its affinity for the substrate poly(Glu/Tyr). Moreover, the interaction of the antibody with the receptor had no repercussion on the ligand binding site as shown by the unaltered IGF-I binding. Taken together our data suggest that the beta-subunit carboxyl-terminal domain of the IGF-I receptor plays a key role in regulating its kinase activity and that the particular sequence recognized by our antipeptide antibody could be involved in negative regulation of receptor functioning.
Effect of Immunotherapy With Bapineuzumab on Cerebrospinal Fluid Biomarker Levels in Patients With Mild to Moderate Alzheimer Disease (2012)

To our knowledge, this study is the first to show that passive Aβ immunotherapy with bapineuzumab results in decreases in CSF T-tau and P-tau, which may indicate downstream effects on the degenerative process. Cerebrospinal fluid biomarkers may be useful to monitor the effects of novel disease-modifying anti-Aβ drugs in clinical trials. TRIAL REGISTRATIONS clinicaltrials.gov Identifier: NCT00112073, EudraCT Identifier: 2004-004120-12, and isrctn.org Identifier: ISRCTN17517446.
Schizophrenia-related and affective personality disorder traits in relatives of probands with schizophrenia and personality disorders (1993)

These results offer preliminary indications that schizotypal personality disorder features present without comorbid affective personality disorder traits may more specifically characterize the personality characteristics familially related to schizophrenia. Furthermore, they indicate that schizotypal personality disorder features as currently defined are found in relatives of patients other than those with schizophrenia or schizotypal personality disorder.
Host range of Exserohilum monoceras, a potential bioherbicide for the control of Echinochloa species (1997)

Fifty-six plant species in 43 genera and 19 families, selected by using the centrifugal phylogenetic method, were screened against Exserohilum monoceras, a fungus collected in the Philippines on Echinochloa colona. Trials were performed under both optimum greenhouse conditions with supplemental 24-h dew and natural field conditions with no dew supplement. The compatibility of host–pathogen interactions was characterized by the time and level of sporulation observed on detached inoculated leaves. All Echinochloa species proved to be highly susceptible to this fungus under optimum greenhouse conditions as well as in the absence of a dew supplement. Rottboellia cochinchinensis was also highly susceptible to this pathogen regardless of the presence of a supplemental dew period. Among the crops tested, only corn seedlings were slightly infected under supplemental 24-h dew conditions, but no disease symptoms were observed on corn in the absence of a dew supplement. Sorghum and sugarcane were hypersensitive to the pathogen under supplemental 24-h dew conditions, but no infection was detected in the absence of a dew supplement. All other species tested were immune to E. monoceras. Data on sporulation on detached leaves from inoculated plants indicated that E. monoceras was weakly compatible with corn. No disease symptoms and no conidia were detected on leaves of trap plants. In the field, E. monoceras produced no symptoms on corn plants. Key words: host range, bioherbicide, Exserohilum monoceras, Echinochloa crus-galli, Echinochloa colona, Echinochloa glabrescens.
Expression of cytokines and chemokine receptors in the cutaneous lesions of erythema multiforme and Stevens-Johnson syndrome/toxic epidermal necrolysis (2006)

We have provided further evidence that TNF-alpha is strongly expressed in SJS/TEN lesions and therefore it may be involved in the epidermal necrosis featured in such diseases. IFN-gamma may play an important role both in EM and SJS/TEN. IL-2, IL-5 and IL-13 may contribute to the cutaneous immunoinflammation in these diseases. Chemokine receptors may be involved strongly in the recruitment of inflammatory cells in lesional skin. In our cases we found a sharp polarization towards a Th1 pattern in EM, while the SJS/TEN lesions showed a mixed Th1/Th2 pattern.
HEPATITIS B EPIDEMIOLOGY AND PREVENTION (1990)

Journal Article HEPATITIS B EPIDEMIOLOGY AND PREVENTION Get access CRAIG N. SHAPIRO, CRAIG N. SHAPIRO Hepatitis Branch, Division of Viral and Rickettsial Diseases, Center for Infectious Diseases, Centers for Disease ControlAtlanta, GA Search for other works by this author on: Oxford Academic PubMed Google Scholar HAROLD S. MARGOLIS HAROLD S. MARGOLIS Hepatitis Branch, Division of Viral and Rickettsial Diseases, Center for Infectious Diseases, Centers for Disease ControlAtlanta, GA Dr. Harold S. Margolis, Hepatitis Branch, Building 6, Room 154 (A-33), Centers for Disease Control, Atlanta, GA 30333 Search for other works by this author on: Oxford Academic PubMed Google Scholar Epidemiologic Reviews, Volume 12, Issue 1, 1990, Pages 221–227, https://doi.org/10.1093/oxfordjournals.epirev.a036055 Published: 01 March 1990 Article history Published: 01 March 1990 Received: 19 March 1990 Revision received: 19 July 1990
Facile Synthesis of Azaarene-Substituted 3-Hydroxy-2-oxindoles via Brønsted Acid Catalyzed sp3 C–H Functionalization (2012)

Brønsted acid catalyzed functionalization of sp(3) C-H bonds in 2-methyl azaarenes has been achieved in the reaction with isatins. This method provides facile synthesis of biologically important azaarene-substituted 3-hydroxy-2-oxindoles in one step in moderate to good yields.
Long-term cardiovascular outcomes of COVID-19 (2022)

The cardiovascular complications of acute coronavirus disease 2019 (COVID-19) are well described, but the post-acute cardiovascular manifestations of COVID-19 have not yet been comprehensively characterized. Here we used national healthcare databases from the US Department of Veterans Affairs to build a cohort of 153,760 individuals with COVID-19, as well as two sets of control cohorts with 5,637,647 (contemporary controls) and 5,859,411 (historical controls) individuals, to estimate risks and 1-year burdens of a set of pre-specified incident cardiovascular outcomes. We show that, beyond the first 30 d after infection, individuals with COVID-19 are at increased risk of incident cardiovascular disease spanning several categories, including cerebrovascular disorders, dysrhythmias, ischemic and non-ischemic heart disease, pericarditis, myocarditis, heart failure and thromboembolic disease. These risks and burdens were evident even among individuals who were not hospitalized during the acute phase of the infection and increased in a graded fashion according to the care setting during the acute phase (non-hospitalized, hospitalized and admitted to intensive care). Our results provide evidence that the risk and 1-year burden of cardiovascular disease in survivors of acute COVID-19 are substantial. Care pathways of those surviving the acute episode of COVID-19 should include attention to cardiovascular health and disease.
Advances in Proline Ligation (2012)

Application of native chemical ligation logic to the case of an N-terminal proline is described. Two approaches were studied. One involved incorporation of a 3R-substituted thiyl-proline derivative. Improved results were obtained from a 3R-substituted selenol function, incorporated in the context of an oxidized dimer.
Interleukin-10 promotes the growth of megakaryocyte, mast cell, and multilineage colonies: analysis with committed progenitors and Thy1loSca1+ stem cells. (1994)

The growth-promoting activities of interleukin-10 (IL-10) were assessed in hematopoietic colony-forming assays. We found that IL-10 failed to support the clonal growth of normal and lineage-depleted (Lin-) bone marrow (BM) cells. Furthermore, IL-10 neither enhanced nor suppressed colony formation by eosinophil, neutrophil, or macrophage progenitors when combined with a variety of factors. IL-10 stimulated a modest increase in erythropoietin (Epo)-dependent erythroid colonies but had no effect on the burst-promoting activities of IL-3. However, the combination of IL-10 plus IL-3 resulted in the enhanced growth of mast cell progenitors. In addition to its mast cell stimulating activity, IL-10 promoted the growth of megakaryocyte (Mk) and Mk-mixed colonies when combined with Epo or with Epo plus IL-3, IL-6, or IL-11. Comparative studies showed that the megakaryocyte potentiating activity of IL-10 is roughly equivalent to that of IL-6 and IL-11. In experiments using Thy1loSca1+ stem cells, IL-10 was shown to enhance the number of cells initiating IL-3-dependent colony formation. IL-10 also costimulated increased colony formation when used with IL-3 and another factor such as IL-1, IL-6, and granulocyte colony-stimulating factor (G-CSF). Cellular analysis of the resulting colonies indicated that IL-10 increases the formation of multilineage colonies containing erythrocytes, megakaryocytes, and/or mast cells. The ability of IL-10 to cooperatively regulate various stages of hematopoietic development is discussed.
HETEROCYCLIC SYNTHESIS WITH NITRILES: SYNTHESIS OF SOME NOVEL THIOPHENE AND THIENO[2,3-d]PYRIMIDINE DERIVATIVES (1992)

Abstract The thiophene derivative 1 reacts with acrylic acid derivatives 2a-c to give N-alkylated derivatives 3a-c which all undergo further hydrolysis to afford N-(thien-2-yl)-β-alanine derivative 6. While 1 reacts with phenyl isothiocyanate to afford the thiourea derivative 8, it reacts with benzoyl isothiocyanate to afford the dihydrothieno [2,3-d]pyrimidine derivative 9. Compound 1 reacts also with diethyl malonate, thiourea 14a and guanidine 14b to afford the thieno[2,3-d] pyrimidine derivatives 13, 15a and 15b respectively. Benzaldehyde condenses with 1 to give the benzylidene derivative 17 which cyclizes with thioglycollic acid to afford 18. Key Words: 5-acetyl-2-amino-4-phenylthiophene-3-carbonitrileβ-alanine derivativethieno[2,3-d]-pyrimidine derivativesN-substituted 2-phenylthiazolidin-4-one derivative
Influence of ethacrynic acid on outflow facility in the monkey and calf eye. (1987)

Living monkeys were perfused via the anterior chamber by the two step constant pressure technique with the sulfhydryl (SH)-reactive diuretic, ethacrynic acid (ECA) at dosages from 0.1 to 1.0 mM. Above 0.37 mM a reproducible increase in outflow facility (C) was observed. At 0.5 mM C increased 115% with ECA compared to a 22% increase in control eyes (n = 9; P less than 0.01). In three monkeys simultaneous perfusion of ECA with cysteine in 10% excess prevented this effect. In enucleated calf eyes at dosages ranging from 0.1 to 0.5 mM ECA a similar increase in outflow facility was demonstrated. Simultaneous perfusion of 0.1 mM ECA with 0.5 mM cysteine blocked this increase in facility. At high dosages (6 mM) of ECA a decrease in C of 35% was observed (P less than 0.01, n = 8). Electron microscopic studies of the perfused monkey eyes did not readily explain the observed facility effects of ECA, except for the occurrence of a small number of breaks in the inner wall endothelium of Schlemm's canal. The juxtacanalicular meshwork appeared normal. Moderate to profound trabecular endothelial cell swelling was observed with ECA alone and with simultaneous cysteine. Morphologic studies performed 4 and 11 weeks after repetitive acute exposure to ECA indicated that the tissues of the outflow pathway appeared normal. The importance of this work is that it points to a new class of drugs that may be used someday to treat glaucoma.(ABSTRACT TRUNCATED AT 250 WORDS)
Raman Spectra of Lignin Model Compounds (2005)

spectroscopy for analyzing lignins and lignin-containing materials, a detailed understanding of lignins ’ Raman spectra needs to be achieved. Although advances made thus far have led to significant growth in application of Raman techniques, further developments are needed to improve upon the existing knowledge. Considering that lignin’s heterogeneous structure consists not only of inter-phenylpropane-unit linkages of carbon-to-carbon and carbon-to-oxygen, but also of side chains with various substituent and functional groups, a study of a large number of representative models is essential. In the present work, 40 lignin models were investigated in the neat state (near-IR FT-Raman and FT-IR), in solution (near-IR FT-Raman), and on cellulose (near-IR FT-Raman). These models represent a large number of substituent/functional groups and sub-structures in lignin- aliphatic and phenolic OH, C=O, CHO, COOH, CH3, OCH3, α,β C=C, furan, and interunit C-O-C and C-C linkages. Raman band positions associated with various groups were identified and Raman frequencies and intensities were compared between the models. For example, for the phenyl group, some of the noteworthy findings were as follows. The intensities of the 1600 (aromatic ring stretch) and 3070 (aromatic C-H stretch) cm-1 bands varied significantly between the models. The position of the 1600 cm-1-Raman-mode was found to be only minimally sensitive to substituents because in about 70 % of the models, including those containing more than 1 phenyl group, the vibrational frequency was confined between 1594 and 1603 cm-1. Similar information was obtained on other functional groups as well. It is hoped that the findings from this study will greatly aid in developing a better understanding of the Raman spectra of lignins and lignocellulosic materials. To fully exploit the value of Raman
Common polymorphisms in the vascular endothelial growth factor gene and colorectal cancer development, prognosis, and survival (2008)

Angiogenesis plays an important role in growth, progression, and metastasis of tumors. The most important regulator of angiogenesis is vascular endothelial growth factor (VEGF). VEGF expression has been associated with advance stage and poor survival of several cancers. In the present study we evaluated the association of functional polymorphisms in the VEGF gene with colorectal cancer development, prognosis, and survival. Three hundred twelve consecutive patients with surgically treated colorectal adenocarcinoma were enrolled in the present study. The genomic DNA was extracted from paraffin-embedded tissue and five VEGF (-2578C>A, -1154G>A, -634G>C, -460T>C, and +936C>T) gene polymorphisms were determined using a polymerase chain reaction-restriction fragment length polymorphism assay. VEGF -2578C>A, -1154G>A, -634G>C, -460T>C, and +936C>T genotype and allele frequencies were similar among patients and controls. There was a trend showing carriers of the -2578A and +936T alleles more frequent among patients with CRC, but these differences did not reach statistical significance. Furthermore, no correlation was found between all these variants and tumor characteristics like size, histological grading, positive regional lymph node metastases or tumor stage. However, the -2578AA, -634CC, and +936TT genotypes found to be related with a significantly lower overall survival in our study. In conclusion, VEGF gene polymorphisms were found to be an independent prognostic marker for Greek CRC patients.
Antiandrogen Bicalutamide Promotes Tumor Growth in a Novel Androgen-Dependent Prostate Cancer Xenograft Model Derived from a Bicalutamide-Treated Patient (2005)

Androgen ablation therapies are effective in controlling prostate cancer. Although most cancers relapse and progress despite androgen ablation, some patients experience antiandrogen withdrawal syndrome, in which those treated with antiandrogen show clinical improvement when antiandrogen is discontinued. Although the androgen receptor (AR) is suggested to play an important role in prostate cancer progression even after the androgen ablation, limited tissue availability for molecular studies and small numbers of human prostate cancer cell lines have restricted prostate cancer research. Here, we describe KUCaP, a novel serially transplantable human prostate cancer xenograft model. We established KUCaP from liver metastatic tissue of a patient treated with antiandrogen bicalutamide. KUCaP expressed the AR with a point mutation at amino acid 741 (tryptophan to cysteine; W741C) in the ligand-binding domain. This mutation was also present in cancerous tissue used for generation of KUCaP. Although the growth of KUCaP in male mice was androgen dependent, bicalutamide aberrantly promoted the growth and prostate-specific antigen production of KUCaP. For the first time, we show the agonistic effect of bicalutamide to a xenograft with clinically induced AR mutation. This bicalutamide-responsive mutant AR will serve in the development of new therapies for androgen ablation-resistant prostate cancers.