gebhart/patrepeval huggingface dataset:
The Heffter Research Institute: Past and Hopeful Future (2014)

This essay describes the founding of the Heffter Research Institute in 1993 and its development up to the present. The Institute is the only scientific research organization dedicated to scientific research into the medical value of psychedelics, and it has particularly focused on the use of psilocybin. The first clinical treatment study was of the value of psilocybin in obsessive-compulsive disorder. Next was a UCLA study of psilocybin to treat end-of-life distress in end-stage cancer patients. While that study was ongoing, a trial was started at Johns Hopkins University (JHU) to study the efficacy of psilocybin in treating anxiety and depression resulting from a cancer diagnosis. Following the successful completion of the UCLA project, a larger study was started at New York University, which is near completion. A pilot study of the value of psilocybin in treating alcoholism at the University of New Mexico also is nearing completion, with a larger two-site study being planned. Other studies underway involve the use of psilocybin in a smoking cessation program and a study of the effects of psilocybin in long-term meditators, both at JHU. The institute is now planning for a Phase 3 clinical trial of psilocybin to treat distress in end-stage cancer patients.
JPEG: Still Image Data Compression Standard (1992)

Foreword. Acknowledgments. Trademarks. Introduction. Image Concepts and Vocabulary. Aspects of the Human Visual Systems. The Discrete Cosine Transform (DCT). Image Compression Systems. JPEG Modes of Operation. JPEG Syntax and Data Organization. Entropy Coding Concepts. JPEG Binary Arithmetic Coding. JPEG Coding Models. JPEG Huffman Entropy Coding. Arithmetic Coding Statistical. More on Arithmetic Coding. Probability Estimation. Compression Performance. JPEG Enhancements. JPEG Applications and Vendors. Overview of CCITT, ISO, and IEC. History of JPEG. Other Image Compression Standards. Possible Future JPEG Directions. Appendix A. Appendix B. References. Index.
Defect reduction mechanisms in the nanoheteroepitaxy of GaN on SiC (2004)

This article describes defect reduction mechanisms that are active during the growth of GaN by nanoheteroepitaxy on (0001) 6H SiC. Nanoheteroepitaxial (NHE) and planar GaN epitaxial films were grown and compared using transmission electron microscopy, photoluminescence, x-ray diffraction, and time resolved photoluminescence. It was found that in addition to the previously reported defect reduction mechanism that results from the high compliance of nanoscale nuclei, other independent defect reduction mechanisms are also active during NHE including: (i) filtering of substrate defects, (ii) improved coalescence at the nanoscale, and (iii) defect termination at local free surfaces. Also, it was found that the biaxial strain in the GaN film could be significantly reduced by using a “grouped” NHE pattern geometry. Time resolved photoluminescence measurements on NHE GaN samples with this geometry showed a more than tenfold increase in carrier lifetime compared to GaN grown on planar SiC.
Intraoperative Femoral Fractures Associated With Cementless Total Hip Arthroplasty (1989)

Between 1982 and 1986, 56 femoral fractures associated with cementless total hip arthroplasty (THA) were evaluated and compared to a randomly selected cementless THA control group without fractures. Depending upon the femoral shaft location, these fractures were classified as Types I, II or III. There were 45 (80%) Type I, 9 (16%) Type II, and 2 (4%) Type III fractures. Patient evaluations were quantified using a modified d'Aubigne-Harris scoring system. Nonparametric statistical methodology was used for fracture and control group comparisons. Treatment protocols were divided into various modalities, depending upon fracture classification. Type I and Type II fractures have no long-term prognostic hazards associated with them (P greater than 0.1), while Type III fractures appear to have analogous clinical results (sample size was too small for statistical analysis).
Root aeration in rice (Oryza sativa): evaluation of oxygen, carbon dioxide, and ethylene as possible regulators of root acclimatizations (2006)

Adventitious roots of rice (Oryza sativa) acclimatize to root-zone O(2) deficiency by increasing porosity, and induction of a barrier to radial O(2) loss (ROL) in basal zones, to enhance longitudinal O(2) diffusion towards the root tip. Changes in root-zone gas composition that might induce these acclimatizations, namely low O(2), elevated ethylene, ethylene-low O(2) interactions, and high CO(2), were evaluated in hydroponic experiments. Neither low O(2) (0 or 0.028 mol m(-3) O(2)), ethylene (0.2 or 2.0 microl l(-1)), or combinations of these treatments, induced the barrier to ROL. This lack of induction of the barrier to ROL was despite a positive response of aerenchyma formation to low O(2) and elevated ethylene. Carbon dioxide at 10 kPa had no effect on root porosity, the barrier to ROL, or on growth. Our findings that ethylene does not induce the barrier to ROL in roots of rice, even though it can enhance aerenchyma formation, shows that these two acclimatizations for improved root aeration are differentially regulated.
Human myosin VIIA responsible for the Usher 1B syndrome: a predicted membrane-associated motor protein expressed in developing sensory epithelia. (1996)

The gene encoding human myosin VIIA is responsible for Usher syndrome type III (USH1B), a disease which associates profound congenital sensorineural deafness, vestibular dysfunction, and retinitis pigmentosa. The reconstituted cDNA sequence presented here predicts a 2215 amino acid protein with a typical unconventional myosin structure. This protein is expected to dimerize into a two-headed molecule. The C terminus of its tail shares homology with the membrane-binding domain of the band 4.1 protein superfamily. The gene consists of 48 coding exons. It encodes several alternatively spliced forms. In situ hybridization analysis in human embryos demonstrates that the myosin VIIA gene is expressed in the pigment epithelium and the photoreceptor cells of the retina, thus indicating that both cell types may be involved in the USH1B retinal degenerative process. In addition, the gene is expressed in the human embryonic cochlear and vestibular neuroepithelia. We suggest that deafness and vestibular dysfunction in USH1B patients result from a defect in the morphogenesis of the inner ear sensory cell stereocilia.
Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer (2010)

Early in F plasmid conjugative transfer, the F relaxase, TraI, cleaves one plasmid strand at a site within the origin of transfer called nic. The reaction covalently links TraI Tyr16 to the 5'-ssDNA phosphate. Ultimately, TraI reverses the cleavage reaction to circularize the plasmid strand. The joining reaction requires a ssDNA 3'-hydroxyl; a second cleavage reaction at nic, regenerated by extension from the plasmid cleavage site, may generate this hydroxyl. Here we confirm that TraI is transported to the recipient during transfer. We track the secondary cleavage reaction and provide evidence it occurs in the donor and F ssDNA is transferred to the recipient with a free 3'-hydroxyl. Phe substitutions for four Tyr within the TraI active site implicate only Tyr16 in the two cleavage reactions required for transfer. Therefore, two TraI molecules are required for F plasmid transfer. Analysis of TraI translocation on various linear and circular ssDNA substrates supports the assertion that TraI slowly dissociates from the 3'-end of cleaved F plasmid, likely a characteristic essential for plasmid re-circularization.
Cardiac outflow tract malformations in chick embryos exposed to homocysteine (2004)

This study demonstrates that homocysteine disturbs apoptosis and myocardialization of the outflow tract, probably by affecting the cardiac neural crest cells.
Contribution of Dithiol Ligands to In Vitro and In Vivo Trypanocidal Activities of Dithiaarsanes and Investigation of Ligand Exchange in an Aqueous Solution (2000)

Twelve new dithiaarsanes were evaluated for their in vitro and in vivo trypanocidal properties in regard to their three parent molecules, 4-amino-phenylarsenoxide, melarsenoxide, and 4-dansylamino-phenylarsenoxide. The most potent dithiaarsane, compound 2b, had a minimum effective concentration of 1.5 nM after 48 h of incubation and at a dose of 0.39 micromol/kg of body weight (0.2 mg/kg) administered subcutaneously cured 100% of mice acutely infected with Trypanosoma brucei brucei CMP. With this model, the chemotherapeutic index of compound 2b was 512, compared to 256 for melarsamine dihydrochloride (Cymelarsan) under the same conditions. With a chronic infection produced by T. brucei brucei GVR, compound 2b cured 100% of mice after treatment at a dose of 25 micromol/kg (12.5 mg/kg) for 4 consecutive days, whereas melarsamine dihydrochloride and potassium melarsonyl (Trimelarsan) cured less than 50% mice at this dose. For both acute and late-stage infections, dithiaarsanes having a melaminophenyl ring exhibited the most-potent trypanocidal activity. Compound 2b is thus one of the most active organoarsenicals described in a mouse trypanosomiasis model. Considering that the main intracellular targets of organoarsenicals are thiol groups, we studied the possibility of ligand exchange between Cymelarsan and several dithiols. In aqueous solution, we observed a rapid exchange of cysteamine from melarsamine with free cysteamine and also with various dithiols always in favor of more stable cyclic derivatives. These ligand exchanges suggest the ability of trivalent organoarsenicals to react with targets such as trypanothione and dihydrolipoic acid. Among several ligands, a 1,3-dimercaptopropane moiety appeared the most suitable for trypanocidal activity.
Construction of a Multihybrid Display System: Flagellar Filaments Carrying Two Foreign Adhesive Peptides (2000)

A multivalent, bifunctional flagellum carrying two different adhesive peptides in separate flagellin subunits within a filament was constructed in Escherichia coli. The inserted peptides were the fibronectin-binding 115-mer D repeat region of Staphylococcus aureus and the 302-mer collagen-binding region of YadA of Yersinia enterocolitica. Western blotting, immunoelectron microscopy, and adhesion tests with hybrid flagella from an in trans-complemented DeltafliC E. coli strain showed that individual filaments consisted of both recombinant flagellins.
The in vitro activity of the tyrosine kinase inhibitor STI571 in BCR–ABL positive chronic myeloid leukaemia cells: synergistic interactions with anti-leukaemic agents (2002)

Chronic myeloid leukaemia is typically characterised by the presence of dysregulated BCR-ABL tyrosine kinase activity, which is central to the oncogenic feature of being resistant to a wide range of cytotoxic agents. We have investigated whether the inhibition of this tyrosine kinase by the novel compound STI571 (formerly CGP57148B) would render K562, KU812 cell lines and chronic myeloid leukaemia-progenitor cells sensitive to induction of cell kill. Proliferation assays showed STI571 to be an effective cytotoxic agent in chronic myeloid leukaemia-derived cell lines (IC(50) on day 5 of 4.6 microg ml(-1) and 3.4 microg ml(-1) for K562 and KU812 respectively) and in leukaemic blast cells (per cent viability on day 3 at 4 microg ml(-1): 55.5+/-8.7 vs 96.4+/-3.7%). STI571 also appeared to specifically target bcr-abl expressing cells, as results from colony forming assays using the surviving cell fraction from STI571-treated peripheral CD34(+) chronic myeloid leukaemia blast cells, indicated a reduction in the expansion of colonies of myeloid lineage, but no effect on normal colony formation. Our data also showed synergy between STI571 and other anti-leukaemic agents; as an example, there were significant increases in per cent cell kill in cell lines cultured with both STI571 and etoposide compared to the two alone (per cent cell kill on day 3: 73.7+/-11.3 vs 44.5+/-8.7 and 17.8+/-7.0% in cultures with STI571 and etoposide alone respectively; P<0.001). This study confirms the central oncogenic role of BCR-ABL in the pathogenesis of chronic myeloid leukaemia, and highlights the role of targeting this tyrosine kinase as a useful tool in the clinical management of the disease.
Parasitologic and Clinical Human Response to Immunoglobulin Administration in Falciparum Malaria (1991)

The protective effect of African IgG antibodies against Plasmodium falciparum malaria was investigated by passive transfer in Thai patients. Sera from 333 African adults were collected in the Cote d'Ivoire and subjected to extensive screening. One hundred fifty-three samples were discarded for safety reasons, and IgG was extracted from those remaining under conditions allowing their use by the intravenous (iv) route. Eight Thai patients with P. falciparum parasitemia were treated by iv inoculation of the IgG: six with a 100 mg/kg dose given over three days, one with a single 20 mg/kg dose, and one with a single 200 mg/kg dose. To ensure a safety margin of at least 48 hours, subjects were chosen among patients having a recrudescent parasitemia following quinine treatment failure at the RI level. At that stage, symptoms were mild or absent and parasitemia was low but increasing (range 4, 200-9,000/microliters). The IgG pool exerted a profound, stage-specific, but non-sterilizing effect on each of the strains tested, and proved to be safe. Asexual parasitemia decreased by a mean 728-fold (range 46-1,086), while gametocytes were unaffected. Clearance of parasites and symptoms was as fast or faster than with drugs, and was consistent in the eight patients treated, suggesting that target antigens were equally expressed in geographically remote isolates. In peripheral blood smears, no mature forms were seen at any time during the followup, which does not support the hypothesis that reversal of cytoadherence occurred. After the disappearance of the transferred antibodies, recrudescent parasites from three patients were found to be susceptible to the same extent (mean decrease of 1,310-fold) to the same IgG preparation, indicating that selection of parasites able to escape the effect of antibodies had not occurred. No adverse side-effects were detected during the followup, which lasted one year.
Comparison Between Noninvasive Indices of Baroreceptor Sensitivity and the Phenylephrine Method in Post–Myocardial Infarction Patients (1998)

The results obtained by means of noninvasive baroreflex sensitivity assessments should not be used in clinical practice as an alternative to those obtained by the phenylephrine method.
Purification and cDNA Cloning of Maize Poly(ADP)-Ribose Polymerase (1998)

Poly(ADP)-ribose polymerase (PADPRP) has been purified to apparent homogeneity from suspension cultures of the maize (Zea mays) callus line. The purified enzyme is a single polypeptide of approximately 115 kD, which appears to dimerize through an S-S linkage. The catalytic properties of the maize enzyme are very similar to those of its animal counterpart. The amino acid sequences of three tryptic peptides were obtained by microsequencing. Antibodies raised against peptides from maize PADPRP cross-reacted specifically with the maize enzyme but not with the enzyme from human cells, and vice versa. We have also characterized a 3.45-kb expressed-sequence-tag clone that contains a full-length cDNA for maize PADPRP. An open reading frame of 2943 bp within this clone encodes a protein of 980 amino acids. The deduced amino acid sequence of the maize PADPRP shows 40% to 42% identity and about 50% similarity to the known vertebrate PADPRP sequences. All important features of the modular structure of the PADPRP molecule, such as two zinc fingers, a putative nuclear localization signal, the automodification domain, and the NAD+-binding domain, are conserved in the maize enzyme. Northern-blot analysis indicated that the cDNA probe hybridizes to a message of about 4 kb.
Myristoylation of the RING Finger Z Protein Is Essential for Arenavirus Budding (2004)

The arenavirus small RING finger Z protein is the main driving force of arenavirus budding. The primary structure of Z is devoid of hydrophobic transmembrane domains, but both lymphocytic choriomeningitis virus (LCMV) and Lassa fever virus Z proteins accumulate near the inner surface of the plasma membrane and are strongly membrane associated. All known arenavirus Z proteins contain a glycine (G) at position 2, which is a potential acceptor site for a myristoyl moiety. Metabolic labeling showed incorporation of [(3)H]myristic acid by wild-type Z protein but not by the G2A mutant. The mutation G2A eliminated Z-mediated budding. Likewise, treatment with the myristoylation inhibitor 2-hydroxymyristic acid inhibited Z-mediated budding, eliminated formation of virus-like particles, and caused a dramatic reduction in virus production in LCMV-infected cells. Budding activity was restored in G2A mutant Z proteins by the addition of the myristoylation domain of the tyrosine protein kinase Src to their N termini. These findings indicate N-terminal myristoylation of Z plays a key role in arenavirus budding.
Basic analysis of AR-coated, partly gain-coupled DFB lasers: the standing wave effect (1992)

A theoretical analysis of distributed feedback (DFB) lasers with mixed gain and index coupling (partly gain-coupled DFB) is given for perfect antireflection (AR) coatings. Analytical expressions for the threshold gain, facet loss, and the relative depth of the standing wave pattern are derived. At the same time the importance of the standing wave effect and its consideration by coupled mode equations is shown. For purely gain-coupled DFB lasers, simple expressions for the effective linewidth enhancement factor and the longitudinal spontaneous emission factor are derived. In addition, various approximations describing the performance of purely gain-coupled DFB lasers are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Variable promoter region CpG island methylation of the putative tumor suppressor gene Connexin 26 in breast cancer (2002)

Intercellular communication via gap junctions is a mechanism for tumor suppression. Connexin 26 (Cx26) is a structural component of gap junctions expressed by breast epithelial cells. Expression levels of Cx26 are reduced in many breast tumors. Methylation-sensitive single-stranded conformation analysis showed variable methylation in the promoter region CpG island in 11 out of 20 (55%) breast cancer patients. Heterogeneity in methylation patterns was observed both between and within tumors. The degree of methylation ranged from a few CpG dinucleotides to almost all the CpG dinucleotides in the analyzed region. The most frequently methylated CpG was in an Sp1 site known to be important for Cx26 gene expression. One of eight breast cancer cell lines (MD-MBA-453) was methylated in the promoter region and did not express Cx26. Treatment of MDA-MB-453 with 5-aza-2'-deoxycytidine resulted in the re-expression of Cx26 mRNA. Methylation of the promoter region is likely to be an important mechanism in modulating the expression of Cx26 in breast cancer.
Conserved Residues Amino-Terminal of Cytoplasmic Tyrosines Contribute to the SHP-1-Mediated Inhibitory Function of Killer Cell Ig-Like Receptors (1999)

The sequence I/VxYxxL, often referred to as an immunoreceptor tyrosine-based inhibition motif (ITIM), binds to the C-terminal Src homology 2 domain of the tyrosine phosphatase SHP-1. Conserved residues N-terminal of the tyrosine are not ordinarily found in other Src homology 2 domain binding motifs. The inhibitory forms of killer cell Ig-like receptors (KIR) contain two ITIMs. The role of each ITIM, and of the conserved residues upstream of the tyrosine, in the inhibition of NK cells was tested by vaccinia virus-mediated expression of mutant KIRs. Substitution of the tyrosine in the membrane-proximal ITIM abrogated the ability of KIR to block Ab-dependent cellular cytotoxicity, whereas mutation of the membrane-distal ITIM tyrosine had little effect. Substitution of the conserved hydrophobic amino acid that was located two residues N-terminal to the tyrosine weakened, but did not eliminate, the function of the receptor. In contrast, these substitutions drastically reduced the amount of SHP-1 immunoprecipitated with KIR, suggesting that weak interactions with SHP-1 may be sufficient for inhibition.
Minimum Word Error Rate Training for Attention-Based Sequence-to-Sequence Models (2018)

Sequence-to-sequence models, such as attention-based models in automatic speech recognition (ASR), are typically trained to optimize the cross-entropy criterion which corresponds to improving the log-likelihood of the data. However, system performance is usually measured in terms of word error rate (WER), not log-likelihood. Traditional ASR systems benefit from discriminative sequence training which optimizes criteria such as the state-level minimum Bayes risk (sMBR) which are more closely related to WER. In the present work, we explore techniques to train attention-based models to directly minimize expected word error rate. We consider two loss functions which approximate the expected number of word errors: either by sampling from the model, or by using N-best lists of decoded hypotheses, which we find to be more effective than the sampling-based method. In experimental evaluations, we find that the proposed training procedure improves performance by up to 8.2% relative to the baseline system. This allows us to train grapheme-based, uni-directional attention-based models which match the performance of a traditional, state-of-the-art, discriminative sequence-trained system on a mobile voice-search task.
Monitoring and Recording of Physiological Data of the Manned Space Flight Program (1965)

This paper propounds the philosophy behind the design of a sensing and data collection system for the handling of low-potential physiological signals used in the determination of astronaut well-being. The experience gained from Project Mercury manned flights and numerous studies performed by the NASA, industry, and university groups has contributed to the establishment of the design criteria. The actual hardware for support of the Gemini manned missions has been designed, built, and flight qualified.
Tandem Asymmetric Cyclopropanation/Cope Rearrangement. A Highly Diastereoselective and Enantioselective Method for the Construction of 1,4-Cycloheptadienes (1998)

Decomposition of vinyldiazoacetates by rhodium(II) (N-dodecylbenzenesulfonyl)prolinate (Rh2(S-DOSP)4, 1) in the presence of dienes results in a direct and highly enantioselective method for the formation of cis-divinylcyclopropanes. Combination of this process with a subsequent Cope rearrangement results in a highly enantioselective synthesis of a variety of cycloheptadienes containing multiple stereogenic centers.