gebhart/patrepeval huggingface dataset:
Ab initio gene identification in metagenomic sequences (2010)

We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed to bypass this difficulty, one effective method is to estimate parameters from dependencies, formed in evolution, between frequencies of oligonucleotides in protein-coding regions and genome nucleotide composition. Original version of the method was proposed in 1999 and has been used since for (i) reconstructing codon frequency vector needed for gene finding in viral genomes and (ii) initializing parameters of self-training gene finding algorithms. With advent of new prokaryotic genomes en masse it became possible to enhance the original approach by using direct polynomial and logistic approximations of oligonucleotide frequencies, as well as by separating models for bacteria and archaea. These advances have increased the accuracy of model reconstruction and, subsequently, gene prediction. We describe the refined method and assess its accuracy on known prokaryotic genomes split into short sequences. Also, we show that as a result of application of the new method, several thousands of new genes could be added to existing annotations of several human and mouse gut metagenomes.
Isolation and characterisation of a human anti-idiotypic scFv used as a surrogate tumour antigen to elicit an anti-HER-2/neu humoral response in mice (2004)

HER-2/neu is a tumour antigen that is overexpressed in human breast tumours. Among the vaccine strategies developed to overcome immune tolerance to self-proteins, vaccination with anti-idiotypic (anti-Id) antibodies has been described as a promising approach for treatment of several malignant diseases. To develop an active immunotherapy for cancer patients positive for HER-2/neu, we investigated immunisation with human anti-Id single-chain fragments (scFv) mimicking the conformation of HER-2/neu protein to induce a humoral response in mice. We selected by phage display two human anti-Id scFv (Ab2beta) directed against trastuzumab F(ab')2 fragments (Ab1), a humanised anti-HER-2/neu monoclonal antibody. Using competitive ELISA and Biacore biosensor analysis, we showed that anti-Id scFv 40 and scFv 69 could inhibit HER-2/neu binding to trastuzumab. Following vaccination of BALB/c mice with the soluble or phage-displayed scFv, Ab3 polyclonal antibodies, and among them Ab1' antibodies able to bind HER-2/neu, were detected in the sera of the immunised mice. These results demonstrate that the human anti-Id scFv could act as a surrogate antigen for HER-2/neu. The present study strongly suggests that the novel 30 kDa human mini-antibody could be used as an anti-idiotype-based vaccine formulation to induce an effective humoral response in patients bearing HER-2/neu-positive tumours.
Towards a national slum upgrading program for Ghana - building on 15 years of efforts to improve the living conditions of the poor in Ghana's cities (2000)

The note provides an outline of slum upgrading projects in Ghana, designed within low cost standards, funded by the central government with assistance from respective local governments. During 1985-1995, basic infrastructure such as roads, drainage works, and water supply for communal needs, improved the livelihoods of urban communities, and, in parallel, another set of upgrading schemes was carried out, through the implementation of several types of infrastructure packaged into one works contract, an approach which reduced costs, and avoided coordination problems. The evolution of urban upgrading is examined through project experiences, featuring key design principles, and identifying its impact on local communities, an impact which has fostered political support, leading the way to a national upgrading program, that will eventually cover all cities, and towns in Ghana.
Les guerres maccabéennes, la résistance armée (2005)

Que faire lorsqu'un grand roi veut soumettre une petite province de son empire a une uniformisation culturelle, economique et religieuse, voulant, au mepris des engagements de ses predecesseurs, la forcer a abandonner ses us et coutumes, sa culture ancestrale et sa religion particuliere ? Telle est la question a laquelle chaque judeen eut a repondre en son âme et conscience a la fin de l'an 167 av. notre ere et qui entrainera le pays dans 25 ans d'une guerre meurtriere qui nous est surtout connue par les deux livres des Maccabees de la Bible grecque, ainsi que par quelques historiens classiques et l'archeologie.
Efficient Synthesis of 4-Cyano 2,3-Dihydrooxazoles by Direct Amination of 2-Alkylidene 3-Oxo Nitriles (2005)

The addition of N-protected O-sulfonyl hydroxylamine derivatives on 2-alkylidene 3-oxo nitrites gives 2,5-disubstituted 4-cyano 2,3-dihydrooxazoles (4-oxazolines) by a practical and efficient synthetic procedure under very mild conditions in high yields. Likely. the formation of N,O-heterocycles proceeds through a domino reaction involving a fast rearrangement of unstable 2-acyl 2-cyano aziridines.
A review of stabilisation works on the wreck of the William Salthouse in Port Phillip Bay (1996)

The William Salthouse in Port Phillip Bay is amongst Victoria's most significant shipwrecks. Since its discovery by sport divers in the early 1980s the archaeological integrity of the site has been threatened by erosion of the sediments in which it rests. In the past ten years the wreck has been subjected to a number of attempts to halt this erosion. This paper reviews the history of stabilization works on the William Salthouse and explain, in detail, the most recent work and its results.
Lexical Approach to College English Teaching (2007)

This paper discusses the lexical approach in college English teaching and learning. The lexical approach can help students learn to use English in an idiomatic way rather than in a Chinese way which may cause misunderstanding or confusion of native English speakers. As for the college English Teaching in China, the lexical approach works better than the traditional word-based teaching and learning. It can help students to learn ”real” or ”authentic” English and improve the students' ability to use English in all-around way.
A Student Experience of Peer Assisted Study Sessions in Physiotherapy (2012)

Peer Assisted Study Sessions (PASS) were introduced as an optional learning experience in a Bachelor of Physiotherapy programme. The aim of this study was to evaluate the use of PASS from the student perspective. Eight third year physiotherapy students who had participated in PASS during their second year of training attended a focus group, at which they provided their perspectives of these PASS sessions. A transciption of the focus group outcomes was analysed qualitatively using the general inductive approach, by two independent reviewers.\nOverall, the students’ perceptions of PASS were positive for their learning, showing that PASS is a useful and effective adjunct to formal teaching for this group of students. Three main themes were identified: learning environment, revision and mastery of skills and clinical application. This study suggests that PASS could play a useful role in an undergraduate physiotherapy programme.
Pharmaceutical Preformulation (1998)

FROM THE PREFACEThis book addresses problems and solutions of formulation and preformulation with which I have concerned myself for 34 years. When I was employed in the pharmaceutical industry I worked at functions, in the 1960's, which were the precursors of preformulation, and my early publications dealt with such matters. In the followin
Diversity in inhibitory effects of IFN-gamma and IFN-alpha A on the induced DNA synthesis of a hairy cell leukemia B lymphocyte clone reflects the nature of the activating ligand (1988)

A hairy cell leukemia population was used as a clonal model for studying the direct immunomodulatory effects of recombinant interferon- alpha A (rIFN-alpha A) and rIFN-gamma on human B-cell proliferation. The leukemic cell population KON was notably quiescent when incubated in medium alone but was induced to significant in vitro DNA synthesis when cultured with any of four activators of human B cells: anti-IgM antibody, Staphylococcus aureus cells (SAC), phorbol myristate acetate (PMA), or B-cell growth factor (BCGF). While both rIFN-gamma and rIFN- alpha A exhibited suppressive effects on these responses, their inhibitory patterns were distinct and reciprocal. Thus, rIFN-gamma exclusively suppressed anti-IgM-and SAC-induced leukemic DNA synthesis, and rIFN-alpha A significantly suppressed only PMA- and BCGF-induced DNA synthesis. The effects of the rIFN preparations were ablated in the presence of IFN type-specific monoclonal antibodies. Kinetic analyses and pulsing studies revealed that inhibition was most notable when cells were exposed concomitantly to IFN and the activating ligand. That the diverse effects of IFN-gamma and IFN-alpha A are manifested on a single B-cell clone was confirmed by Southern blot analysis of restriction enzyme-digested KON cell DNA with a JH-specific probe. These studies suggest that the therapeutic potential of the two types of IFN may be influenced by the nature of the extracellular ligands in the leukemic mileau that promote leukemic clonal expansion.
Gefitinib or Carboplatin–Paclitaxel in Pulmonary Adenocarcinoma (2009)

Gefitinib is superior to carboplatin-paclitaxel as an initial treatment for pulmonary adenocarcinoma among nonsmokers or former light smokers in East Asia. The presence in the tumor of a mutation of the EGFR gene is a strong predictor of a better outcome with gefitinib. (ClinicalTrials.gov number, NCT00322452.)
Direct observation of preferential bond fission by excitation of a vibrational fundamental: Photodissociation of HOD (0,0,1) (1990)

The 193 nm photodissociation of individual rotational levels of HOD molecules excited with one quantum of O–H stretching vibrational energy is described. Stimulated Raman excitation and coherent anti-Stokes Raman scattering are used to prepare and detect, respectively, the (0,0,1) vibrationally excited HOD. The OD and OH fragments are detected by laser induced fluorescence. The photodissociation of the HOD (0,0,1) molecules yields at least three times more OD than OH.
Uncatalyzed polymerization of bistriazolinediones with electron‐rich aromatic compounds via electrophilic aromatic substitution (1989)

Abstract The reaction of 4‐substituted‐1,2,4‐triazoline‐3,5‐diones(4R‐TD's), i.e., MeTD(4‐methyl substituted) and PhTD(4‐Phenyl substituted) with electron rich aromatic compounds were investigated. N , N ‐Dimethylaniline undergoes reaction instantaneously with MeTD and PhTD. Electrophilic aromatic substitution occurred at room temperature at the para position without use of any catalyst. N , N , N ′, N ′‐tetramethyl‐ m ‐phenylenediamine (TMPDA) undergoes reaction with 2 mol of PhTD and MeTD which lead to the formation of 2:1 adducts in high yields. These compounds were fully characterized by IR, 13 C‐NMR, 1 H‐NMR and elemental analysis and were used as model compounds. The reaction of bistriazolinediones with TMPDA was performed in dimethylformamid at room temperature. The reactions are exothermic, fast, and gave novel polymer structures via electrophilic aromatic substitution. Some physical properties and structural characterization of these new polymers have been studied, and will be reported.
Atroposelective Synthesis of Axially Chiral Biaryl Compounds (2005)

A rotationally hindered and thus stereogenic biaryl axis is the structurally and stereochemically decisive element of a steadily growing number of natural products, chiral auxiliaries, and catalysts. Thus, it is not surprising that significant advances have been made in the asymmetric synthesis of axially chiral biaryl compounds over the past decade. In addition to the classic approach (direct stereoselective aryl-aryl coupling), innovative concepts have been developed in which the asymmetric information is introduced into a preformed, but achiral-that is, symmetric or configurationally labile-biaryl compound, or in which an aryl--C single bond is stereoselectively transformed into an axis. This Review classifies these strategies according to their underlying concepts and critically evaluates their scope and limitations with reference to selected model reactions and applications. Furthermore, the preconditions required for the existence of axial chirality in biaryl compounds are discussed.
Open-irrigated laser catheter ablation: relationship between the level of energy, myocardial thickness, and collateral damages in a dog model (2013)

To avoid unwanted effects during laser catheter ablation by using an open-irrigated laser catheter energy delivery must be adapted to the thickness of the myocardial wall. Light control system and a transoesophageal light sensor may help reduce the risks of myocardial and collateral damages.
45.5: A System LCD with Optical Input Function using Infra‐Red Backlight Subtraction Scheme (2010)

Abstract We describe a System LCD with optical input function using infra‐red backlight subtraction scheme. By combining an “infrared backlight subtraction scheme” with a high sensitivity “active capacitor” circuit we have achieved a sensor operation robust to ambient conditions and with low power consumption suitable for integration into mobile products.
Acute Infection with Venezuelan Equine Encephalitis Virus Replicon Particles Catalyzes a Systemic Antiviral State and Protects from Lethal Virus Challenge (2021)

The host innate immune response provides a critical first line of defense against invading pathogens, inducing an antiviral state to impede the spread of infection. While numerous studies have documented antiviral responses within actively infected tissues, few have described the earliest innate response induced systemically by infection. Here, utilizing Venezuelan equine encephalitis virus (VEE) replicon particles (VRP) to limit infection to the initially infected cells in vivo, a rapid activation of the antiviral response was demonstrated not only within the murine draining lymph node, where replication was confined, but also within distal tissues. In the liver and brain, expression of interferon-stimulated genes was detected by 1 to 3 h following VRP footpad inoculation, reaching peak expression of >100-fold over that in mock-infected animals. Moreover, mice receiving a VRP footpad inoculation 6, 12, or 24 h prior to an otherwise lethal VEE footpad challenge were completely protected from death, including a drastic reduction in challenge virus titers. VRP pretreatment also provided protection from intranasal VEE challenge and extended the average survival time following intracranial challenge. Signaling through the interferon receptor was necessary for antiviral gene induction and protection from VEE challenge. However, VRP pretreatment failed to protect mice from a heterologous, lethal challenge with vesicular stomatitis virus, yet conferred protection following challenge with influenza virus. Collectively, these results document a rapid modulation of the host innate response within hours of infection, capable of rapidly alerting the entire animal to pathogen invasion and leading to protection from viral disease.
Identifying and reducing critical lag in finite element simulations (1996)

End-to-end lag time can undermine the effectiveness of interactive displays. Analyzing lag components for an FES indicated that simulation time is the critical component.
Segmental motion of ferroelectric liquid crystal polymer and elastomer during electro-optical switching (1998)

Application of both the conservative rapid scan and a novel step-scan Fourier-transform spectroscopy enables us to follow the intra- and intermolecular motion of ferroelectric liquid crystalline polymers and elastomers during electro- optical switching on a time scale from seconds down to microseconds. It has been detected that although all molecular parts move synchronously in course of the switching, the amplitude of such motions is different. The obtained results are discussed in terms of the role played by the molecular segments during the process of reorientation.
To Protect and to Preserve: Novel Preservation Strategies for Extracellular Vesicles (2018)

Extracellular vesicles (EVs)-based therapeutics are based on the premise that EVs shed by stem cells exert similar therapeutic effects and these have been proposed as an alternative to cell therapies. EV-mediated delivery is an effective and efficient system of cell-to-cell communication which can confer therapeutic benefits to their target cells. EVs have been shown to promote tissue repair and regeneration in various animal models such as, wound healing, cardiac ischemia, diabetes, lung fibrosis, kidney injury, and many others. Given the unique attributes of EVs, considerable thought must be given to the preservation, formulation and cold chain strategies in order to effectively translate exciting preclinical observations to clinical and commercial success. This review summarizes current understanding around EV preservation, challenges in maintaining EV quality, and also bioengineering advances aimed at enhancing the long-term stability of EVs.
The Clathrin Adaptor Complex AP-1 Binds HIV-1 and MLV Gag and Facilitates Their Budding (2007)

Retroviral assembly is driven by Gag, and nascent viral particles escape cells by recruiting the machinery that forms intralumenal vesicles of multivesicular bodies. In this study, we show that the clathrin adaptor complex AP-1 is involved in retroviral release. The absence of AP-1mu obtained by genetic knock-out or by RNA interference reduces budding of murine leukemia virus (MLV) and HIV-1, leading to a delay of viral propagation in cell culture. In contrast, overexpression of AP-1mu enhances release of HIV-1 Gag. We show that the AP-1 complex facilitates retroviral budding through a direct interaction between the matrix and AP-1mu. Less MLV Gag is found associated with late endosomes in cells lacking AP-1, and our results suggest that AP-1 and AP-3 could function on the same pathway that leads to Gag release. In addition, we find that AP-1 interacts with Tsg101 and Nedd4.1, two cellular proteins known to be involved in HIV-1 and MLV budding. We propose that AP-1 promotes Gag release by transporting it to intracellular sites of active budding, and/or by facilitating its interactions with other cellular partners.
Absolute phase image reconstruction: a stochastic nonlinear filtering approach (1998)

This paper formulates and proposes solutions to the problem of estimating/reconstructing the absolute (not simply modulo-2pi) phase of a complex random field from noisy observations of its real and imaginary parts. This problem is representative of a class of important imaging techniques such as interferometric synthetic aperture radar, optical interferometry, magnetic resonance imaging, and diffraction tomography. We follow a Bayesian approach; then, not only a probabilistic model of the observation mechanism, but also prior knowledge concerning the (phase) image to be reconstructed, are needed. We take as prior a nonsymmetrical half plane autoregressive (NSHP AR) Gauss-Markov random field (GMRF). Based on a reduced order state-space formulation of the (linear) NSHP AR model and on the (nonlinear) observation mechanism, a recursive stochastic nonlinear filter is derived, The corresponding estimates are compared with those obtained by the extended Kalman-Bucy filter, a classical linearizing approach to the same problem. A set of examples illustrate the effectiveness of the proposed approach.
Battling breast cancer (2005)

In Brief Surgical treatments are less drastic than in the past, and new treatments are zeroing in on tumors and causing fewer adverse effects. Yet the disease still strikes fear in the hearts of women everywhere. Read about new approaches to battling this deadly foe and how you can help your patients conquer their fears. Despite advances in surgical and nonsurgical treatments, breast cancer still strikes fear in the hearts of women everywhere. Read about new ways to fight this deadly foe and learn how to help your patients overcome their fears.
U1 small nuclear ribonucleoprotein immune complexes induce type I interferon in plasmacytoid dendritic cells through TLR7 (2005)

Plasmacytoid dendritic cells (PDCs), which produce IFN-alpha in response to autoimmune complexes containing nuclear antigens, are thought to be critically involved in the pathogenesis of systemic lupus erythematosus (SLE). One of the immunostimulatory components of SLE immune complexes (SLE-ICs) is self DNA, which is recognized through Tlr9 in PDCs and B cells. Small nuclear ribonucleoproteins (snRNPs) are another major component of SLE-ICs in 30% to 40% of patients. In this study, we show that murine PDCs are activated by purified U1snRNP/anti-Sm ICs to produce IFN-alpha and proinflammatory cytokines and to up-regulate costimulatory molecules. The induction of IFN-alpha and IL-6 by U1snRNPs in murine bone marrow-derived PDCs required the presence of intact U1RNA and was largely dependent on Tlr7 but independent of Tlr3. Intracellularly delivered isolated U1snRNA and oligoribonucleotides derived from the stem loop regions and the Sm-binding site of U1snRNA efficiently induced IFN-alpha and IL-6 in Flt3L-cultured DCs in a Tlr7-dependent manner. The U1snRNA component of U1snRNP immune complexes, found in patients with SLE, acts as an endogenous "self" ligand for Tlr7 and triggers IFN-alpha and IL-6 production in PDCs.
Tumor Necrosis Factor Regulates v 5 Integrin Expression by Osteoclast Precursors in Vitro and in Vivo (2000)

Early osteoclast precursors, in the form of murine bone marrow macrophages (BMMs), while expressing no detectableα vβ3 integrin, contain abundantα vβ5 and attach to matrix in anα v integrin-dependent manner. Furthermore,α vβ5 expression by osteoclast precursors progressively falls as they assume the resorptive phenotype. We find the osteoclastogenic agent, tumor necrosis factor-α, (TNF) down-regulates αvβ5 expression by BMMS via attenuation of β5 messenger RNA (mRNA) t1/2. Using BMMs from TNF receptor knockout mice we establish the p55 receptor transmits the β5 suppressive effect. The functional implications of TNF-mediated αvβ5 down-regulation are underscored by the capacity of an αv inhibitory peptide mimetic to prevent spreading by BMMs expressing abundantα vβ5 while failing to impact those in which the integrin has been diminished by TNF. Finally, β5 mRNA in BMMs of wild-type mice administered lipopolysaccharide (LPS) progressively falls with time of in vivo treatment. Alternatively, β5 mRNA does not decline in BMMs of LPS-treated mice lacking both TNF receptors, documenting down-regulation of the β5 integrin subunit, in vivo, is mediated by TNF. Thus, matrix attachment of osteoclast precursors and mature osteoclasts are governed by distinctα v integrins which are differentially regulated by specific cytokines.