gebhart/patrepeval huggingface dataset:
A 12-bit successive-approximation-type ADC with digital error correction (1986)

A correction algorithm has been implemented that gives an almost twofold improvement in conversion speed without loss of accuracy or changes to the analog circuitry of a slower design. The design of a smart successive-approximation register chip, which has been fabricated in a double poly CMOS process and takes up 18 mil/SUP 2/ in die area, is described. The area is 13% larger than that of an A/D converter utilizing the same analog chip but a conventional digital chip without error correction. A speed improvement from 12 to 7 /spl mu/s was obtained with digital error correction.
Two complementary methods of assessing periodontal bone level in rats (1989)

Several methods have been applied to measure periodontal disease in rats. The purpose of the present study was to test the reproducibility of a morphometric and a radiographic method and to describe the correlation between the two methods. Periodontal bone loss on 25 defleshed rat heads was assessed under microscopic by measuring the distances from the cementoenamel junction to the alveolar bone crest at 36 buccal sites in each animal. On magnified radiographs from 25 rat mandibles periodontal bone support was expressed by the ratio apex-deepest bony defect: apex-cusp tip distally on first molars. All measurements were performed blind and in duplicate on two separate occasions. The bilateral 95% confidence limits for the error of method of measurement were estimated from the t-distribution. In a second experiment 50 rat heads were assessed by both methods, and the correlation between the recordings was estimated by the Spearman rank correlation analysis. Compared to the considerable total variation in the material, the variations due to error of methods of measurement were small, i.e. the reproducibility of both methods was satisfactory. A significant correlation was found between the methods. Since the morphometric method mainly measures horizontal bone loss, whereas the radiographic method detects intrabony interproximal defects, it is concluded that future studies would benefit from applying both methods to assess alveolar bone loss in rats.
Biogenesis of the Gram-Negative Bacterial Outer Membrane (2007)

The cell envelope of gram-negative bacteria consists of two membranes, the inner and the outer membrane, that are separated by the periplasm. The outer membrane consists of phospholipids, lipopolysaccharides, integral membrane proteins, and lipoproteins. These components are synthesized in the cytoplasm or at the inner leaflet of the inner membrane and have to be transported across the inner membrane and through the periplasm to assemble eventually in the correct membrane. Recent studies in Neisseria meningitidis and Escherichia coli have led to the identification of several machineries implicated in these transport and assembly processes.
Binding of the Positron Emission Tomography Tracer Pittsburgh Compound-B Reflects the Amount of Amyloid-β in Alzheimer's Disease Brain But Not in Transgenic Mouse Brain (2005)

During the development of in vivo amyloid imaging agents, an effort was made to use micro-positron emission tomography (PET) imaging in the presenilin-1 (PS1)/amyloid precursor protein (APP) transgenic mouse model of CNS amyloid deposition to screen new compounds and further study Pittsburgh Compound-B (PIB), a PET tracer that has been shown to be retained well in amyloid-containing areas of Alzheimer's disease (AD) brain. Unexpectedly, we saw no significant retention of PIB in this model even at 12 months of age when amyloid deposition in the PS1/APP mouse typically exceeds that seen in AD. This study describes a series of ex vivo and postmortem in vitro studies designed to explain this low retention. Ex vivo brain pharmacokinetic studies confirmed the low in vivo PIB retention observed in micro-PET experiments. In vitro binding studies showed that PS1/APP brain tissue contained less than one high-affinity (K(d) = 1-2 nm) PIB binding site per 1000 molecules of amyloid-beta (Abeta), whereas AD brain contained >500 PIB binding sites per 1000 molecules of Abeta. Synthetic Abeta closely resembled PS1/APP brain in having less than one high-affinity PIB binding site per 1000 molecules of Abeta, although the characteristics of the few high-affinity PIB binding sites found on synthetic Abeta were very similar to those found in AD brain. We hypothesize that differences in the time course of deposition or tissue factors present during deposition lead to differences in secondary structure between Abeta deposited in AD brain and either synthetic Abeta or Abeta deposited in PS1/APP brain.
Aerial Simultaneous Localization and Mapping Using Earth's Magnetic Anomaly Field (2019)

Instances of global navigation satelite system (GNSS) spoofing and jamming have emphasized the need for alternative navigation methods. A fusion of methods is required to fill the resulting gaps from Global Positioning System (GPS)-denied circumstances. Aerial navigation by magnetic map-matching has been demonstrated as a viable GPS-alternative inertial navigation system (INS)-aiding technique, but requires an accurate magnetic map which is not always available. Magnetic map availability and resolution varies widely around the globe. Removing the dependency on prior survey maps extends the benefits of aerial magnetic navigation methods to small unmanned aerial systems (sUAS) at lower altitudes where magnetic maps are especially undersampled or unavailable. In this paper, a common simultaneous localization and mapping (SLAM) algorithm known as FastSLAM was modified to scalar magnetic measurements to constrain a drifting navigation-grade INS to tens of meters in a one-hundred minute flight without the use of a prior magnetic map. Aerial SLAM using Earth’s magnetic anomaly field provides a GPS-alternative navigation method that is globally persistent, impervious to jamming or spoofing, stealthy, and locally accurate to tens of meters without the need for a magnetic map.
Synthesis of oligodeoxyribonucleotides containing degenerate bases and their use as primers in the polymerase chain reaction (1992)

Heptadecaoligodeoxyribonucleotides containing one or more of the bases, 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (P), 2-amino-6-methoxyaminopurine (K), and hypoxanthine (I) and combinations of P with K and I have been synthesised on a DNA synthesiser. The stability of duplexes containing these basemodified oligomers with P/A, P/G, K/C and K/T; P/A, P/G, I/C, I/T and I/A, I/G, I/C, I/T base pairs were compared by measuring their melting transition (Tm) values. Oligomers containing both P and K and P and I were more stable than those with I alone or with mismatches. These oligomers together with one with a P base at the 3'-end were used as primers in polymerase chain reaction (PCR) experiments. They were all effective primers except one with I alone and a triple mismatch. Thus the use of the degenerate bases P and K in primer design is established.
Structural studies on myosin II: Communication between distant protein domains (1997)

Understanding how chemical energy is converted into directed movement is a fundamental problem in biology. In higher organisms this is accomplished through the hydrolysis of ATP by three families of motor proteins: myosin, dynein and kinesin. The most abundant of these is myosin, which operates against actin and plays a central role in muscle contraction. As summarized here, great progress has been made towards understanding the molecular basis of movement through the determination of the three-dimensional structures of myosin and actin and through the establishment of systems for site-directed mutagenesis of this motor protein. It now appears that the generation of movement is coupled to ATP hydrolysis by a series of domain movements within myosin.
High-throughput rare cell separation from blood samples using steric hindrance and inertial microfluidics (2014)

The presence and quantity of rare cells in the bloodstream of cancer patients provide a potentially accessible source for the early detection of invasive cancer and for monitoring the treatment of advanced diseases. The separation of rare cells from peripheral blood, as a "virtual and real-time liquid biopsy", is expected to replace conventional tissue biopsies of metastatic tumors for therapy guidance. However, technical obstacles, similar to looking for a needle in a haystack, have hindered the broad clinical utility of this method. In this study, we developed a multistage microfluidic device for continuous label-free separation and enrichment of rare cells from blood samples based on cell size and deformability. We successfully separated tumor cells (MCF-7 and HeLa cells) and leukemic (K562) cells spiked in diluted whole blood using a unique complementary combination of inertial microfluidics and steric hindrance in a microfluidic system. The processing parameters of the inertial focusing and steric hindrance regions were optimized to achieve high-throughput and high-efficiency separation, significant advantages compared with existing rare cell isolation technologies. The results from experiments with rare cells spiked in 1% hematocrit blood indicated >90% cell recovery at a throughput of 2.24 × 10(7) cells min(-1). The enrichment of rare cells was >2.02 × 10(5)-fold. Thus, this microfluidic system driven by purely hydrodynamic forces has practical potential to be applied either alone or as a sample preparation platform for fundamental studies and clinical applications.
Ice nucleating activity of Pseudomonas syringae and Erwinia herbicola (1983)

Chemical and biological properties of the ice nucleating sites of Pseudomonas syringae, strain C-9, and Erwinia herbicola have been characterized. The ice nucleating activity (INA) for both bacteria was unchanged in buffers ranging from pH 5.0 to 9.2, suggesting that there were no essential groups for which a change in charge in this range was critical. The INA of both bacteria was also unaffected by the addition of metal chelating compounds. Borate compounds and certain lectins markedly inhibited the INA of both types of bacterial cells. Butyl borate was not an inhibitor, but borate, phenyl borate, and m-nitrophenyl borate were, in order, increasingly potent inhibitors. These compounds have a similar order of affinity for cis hydroxyls, particularly for those found on sugars. Lentil lectin and fava bean lectin, which have binding sites for mannose or glucose, inhibited the INA of both bacteria. All other lectins examined had no effect. The inhibition of INA by these two types of reagents indicate that sugar-like groups are at or near the ice nucleating site. Sulfhydryl reagents were potent inhibitors of the INA of both bacteria. When treated with N-ethylmaleimide, p-hydroxymercuribenzoate, or iodoacetamide, the INA was irreversibly inhibited by 99%. The kinetics of inactivation with N-ethylmaleimide suggested that E. herbicola cells have at least two separate ice nucleating sites, whereas P. syringae cells have possibly four or more separate sites. The effect of infection with a virulent phage (Erh 1) on the INA of E. herbicola was examined. After multiple infection of a bacterial culture the INA was unchanged until 40 to 45 min, which was midway through the 95-min latent period. At that time, the INA activity began falling and 99% of the INA was lost by 55 min after infection, well before any cells had lysed. This decrease in INA before lysis is attributed to phage-induced changes in the cell wall.
Colour Doppler Imaging to Evaluate the Action of a Drug in Ocular Pathology (1995)

Colour Doppler imaging is a recent advance in ultrasonography. It allows simultaneous two-dimensional imaging of structures and evaluation of blood flow. Retinal vascular pathologies, macular degeneration, endobulbar tumours, and ischaemic vascular diseases can be analyzed by colour Doppler imaging. Moreover, it offers the possibility of evaluating the vascular effects of a drug and to monitor them in time. We have, therefore, carried out a study using colour Doppler imaging to evaluate a drug capable of acting on the vascular wall in patients with macular degeneration or diabetic retinopathy. The results show that this drug, obtained by enzymatic hydrolysis of bovine factor VIII (Vueffe; Laboratory Baldacci S.p.A., Pisa, Italy), induces a significant increase in blood flow and in retinal central artery systolic speed.
Stuck-Free Conformance Theory for CCS (2004)

We present a novel refinement relation (stuck-free conformance) for CCS processes, which satisfies the substitutability property: If an implementation I conforms to a specification S, then C[S] stuck-free implies C[I] stuck-free, on any selected names ~a and for all CCS contexts C. Stuck-freedom is related to the CSP notion of deadlock, but it is more discriminative by taking orphan messages in asynchronous systems into account. We prove that conformance is a precongruence, i.e., it is preserved by all CCS contexts, thereby supporting modular refinement. We distinguish conformance from the related preorders, stable failures refinement in CSP and refusal preorder in CCS. Finally, we consider a family of parameterized refinement relations that can be generated from the format of our definition of stuck-free conformance.
Total Synthesis of ArylomycinA<sub>2</sub>, a Signal Peptidase I (SPase I) Inhibitor (2008)

A concise total synthesis of arylomycin A2 was accomplished featuring a key intramol. Suzuki-Miyaura reaction for the formation of the 14-membered meta,meta-cyclophane and direct coupling of a fully elaborated peptide side-chain with the macrocyclic core. [on SciFinder (R)]
CoSaMP: Iterative signal recovery from incomplete and inaccurate samples (2008)

Compressive sampling offers a new paradigm for acquiring signals that are compressible with respect to an orthonormal basis. The major algorithmic challenge in compressive sampling is to approximate a compressible signal from noisy samples. This paper describes a new iterative recovery algorithm called CoSaMP that delivers the same guarantees as the best optimization-based approaches. Moreover, this algorithm offers rigorous bounds on computational cost and storage. It is likely to be extremely efficient for practical problems because it requires only matrix-vector multiplies with the sampling matrix. For many cases of interest, the running time is just O(N*log^2(N)), where N is the length of the signal.
Comparison of Methods for Isolating High Quality DNA and RNA from an Oleaginous Fungus Cunninghamella bainieri Strain 2a1 (2007)

A number of protocols have been reported for efficient fungal DNA and RNA isolation. However, many of these methods are often designed for certain groups or morphological forms of fungi and, in some cases, are species dependent. In this report, we compared four published protocols for DNA isolation from a locally isolated oleaginous fungus, Cunninghamella bainieri strain 2a1. These protocols either involved the use of polyvinyl pyrrolidone (PVP), hexacetyltrimethylammonium bromide (CTAB) or without using PVB or CTAB. For RNA isolation, we tested two published protocols, one of which is based on TRI REAGENT (Molecular Research Center, USA) and another is simple method employing phenol for RNA extraction and LiCl for precipitation. We found that the protocol involving the use of CTAB produced the highest genomic DNA yield with the best quality compared to other protocols. In the presence of CTAB, unwanted polysaccharides were removed and this method yielded an average amount of 816 12.2 g DNA/g mycelia with UV absorbance ratios A260/280 and A260/230 of 1.67 0.64 and 1.97 0.23, respectively. The genomic DNA isolated via this protocol is also suitable for PCR amplification and restriction enzyme digestion. As for RNA isolation, the method involving phenol extraction and LiCl precipitation produced the highest yield of RNA with an average amount of 372 6.0 g RNA/g mycelia. The RNA appears to be relatively pure since it has UV absorbance ratios A260/280 and A260/230 of 1.89 2.00 and 1.99 0.03, respectively. Finally, we have demonstrated that this method could produce RNA of sufficient quality for RT-PCR that amplified a 600 bp fragment of 12-fatty acid desaturase gene in C. bainieri.
Synthesis, characterization, and immunogenicity in mice of <i>Shigella sonnei</i> O-specific oligosaccharide-core-protein conjugates (2009)

Shigellosis, an enteric disease, is on the World Health Organization's priority prevention list. In one study, the Shigella sonnei O-specific polysaccharide (O-SP)-protein conjugate showed 72% protection against disease in Israeli army recruits exposed to high rates (8-14%) of infection. The protection was related to vaccine-induced IgG anti-O-SP levels. Synthetic oligosaccharides of Shigella dysenteriae type 1, bound by their reducing ends to a carrier protein ("sun"-type configuration), induced significantly higher antibody levels than the native O-SP bound to protein by multiple-point attachments ("lattice"-type configuration). Attempts to synthesize the S. sonnei O-SP based oligosaccharides were not successful. Here, we describe the isolation, characterization, and conjugation of low-molecular-mass O-SP-core (O-SPC) fragments. The O-SPC fragments were bound by their reducing ends similar to the preparation of the synthetic S. dysenteriae type 1 conjugates. The O-SPC conjugates used oxime linkages between the terminal Kdo residues at the reducing ends of the S. sonnei saccharides and aminooxy linkers bound to BSA or a recombinant diphtheria toxin. The coupling reaction was carried out at a neutral pH and room temperature. IgG antibody levels induced in young outbred mice by the S. sonnei O-SPC conjugates were significantly higher then those elicited by the O-SP conjugates. Accordingly, we propose to evaluate clinically these conjugates.
Lactic acid bacteria: microbiology and functional aspects. (1998)

Lactic acid bacteria - classification and physiology industrial use and production of lactic acid bacteria stability of lactic acid bacteria in fermented milk lactic acid bacteria in cereal-based foods genetic modification of lactic acid bacteria lactic acid bacteria in health and disease lactic acid bacteria and immune modulation lactic acid bacteria and intestinal drugs and cholesterol metabolism lactic acid microflora in the human microbial ecosystem and its development prebiotic substrates and lactic acid bacteria lactic acid bacteria - an approach for detoxification of aflatoxias safety of probiotic bacteria bacteriophages and lactic acid bacteria lactic acid bacteria as animal probiotics lactobacilllus reuteri - an effective and probiotic action the other animals bifidobacteria and probiotic action the potential of propionibacteria spp. as probiotics future aspects of research and product development on lactic acid bacteria.
Fingerprint card classification with statistical feature integration (2002)

This paper describes a fingerprint classification algorithm for an automated fingerprint identification system with a large-size ten-print card database. The classification algorithm determines a fingerprint's pattern category based on a ridge structure analysis and a direction-based neural network, and computes additional feature characteristics such as core-delta distance, along with confidence indexes associated with each feature. A card preselector then integrates the set of obtained features after weighting them according to the features expected error and inherent selection capability, calculates the card similarity based on feature differences, statistically evaluates the conditional probability of each pair being a correct match, and selects the most similar subset of the database as candidates for minutiae matching. The experimental results confirm that effective classification capability of 0.2% false acceptance with 2% false rejection has been achieved.
Prospective evaluation of oral mucositis in patients receiving myeloablative conditioning regimens and haemopoietic progenitor rescue (2000)

Four hundred and twenty-nine patients received myeloablative chemotherapy for solid and haematological malignancies in a bone marrow transplantation unit. Regimens appropriate to the tumour type were administered and haemopoietic reconstitution was achieved with peripheral blood progenitor cells (PBPC; n = 275), autologous bone marrow (auto-BMT; n = 69) or allogeneic bone marrow (allo-BMT; n = 85). World Health Organization (WHO) oral mucositis scores were collected prospectively from the start of chemotherapy (d 1) until d 28 or discharge. Oral mucositis (OM) was experienced by 425 (99%) patients and in 289 (67.4%) this was grade III or IV. Strong opiate analgesia was prescribed for a median of 6 d to 47% of patients. Univariate analysis suggested that the area under the OM curve (AUC; sum of daily mucositis grades, d 1-28) was associated with the myeloablative regimen, haemopoietic progenitor source (PBPC > allo-BMT > auto-BMT), use of myeloid growth factors and age. Multivariate analysis showed that the only independent risk factor for mucositis was the conditioning regimen (P < 0.00005). The mean OM AUC for high-dose melphalan (HDM) regimens (52 grade-days) exceeded busulphan (41), busulphan-cyclophosphamide (35), cyclophosphamide-total body irradiation (TBI) (34), cyclophosphamide-carmustine (BCNU) (20) and cyclophosphamide-etoposide-carmustine (CVB) (19). HDM regimens resulted in the highest mean peak OM (3.6), followed by busulphan regimens (2.6), cyclophosphamide/TBI (2.3) and cyclophosphamide-carmustine and CVB (1.4). Busulphan produced significantly delayed OM (median 3 d; P < 0.00005). There was a linear association between the area under the OM curve for each treatment group and the time to reach grade 3 OM (P < 0.00005), but no association with the time to reach grade 4 neutropenia (P = 0.24) or thrombocytopenia (P = 0.73), implying that haematological and mucosal toxicity are not associated. The cytotoxic regimen is the most significant determinant of OM. Studies investigating agents to ameliorate mucosal toxicity should be stratified according to cytotoxic regimen.
Hyaluronan Constitutively Regulates ErbB2 Phosphorylation and Signaling Complex Formation in Carcinoma Cells (2005)

Hyaluronan is enriched in many types of human cancers, and manipulations of hyaluronan expression or interactions have a major influence on tumor progression in animal models. Increased ErbB2 activity is characteristic of several cancers and is responsible for many aspects of malignant cell behavior in these cancers. In this study we show that constitutively high levels of active, i.e. autophosphorylated, ErbB2 in HCT116 colon carcinoma cells and TA3/St mammary carcinoma cells are dependent on endogenous hyaluronan-CD44 interaction. Dependence on hyaluronan-CD44 interaction was demonstrated by the administration of hyaluronan oligomers, experimentally induced expression of soluble CD44, and small interfering RNA knockdown of CD44 expression. On the other hand, increasing hyaluronan production by overexpression of hyaluronan synthase 2 or emmprin causes elevated ErbB2 phosphorylation in MCF-7 mammary carcinoma cells, which normally exhibit low levels of ErbB2 activity. Furthermore, in HCT116 and TA3/St cells, inhibition of endogenous hyaluronan-CD44 interaction causes disassembly of a constitutive, lipid raft-associated, signaling complex containing phosphorylated ErbB2, CD44, ezrin, phosphoinositide 3-kinase, and the chaperone molecules, Hsp90 and cdc37. Stimulation of hyaluronan production in MCF-7 cells induces assembly of this complex. We conclude that hyaluronan regulates ErbB2 activity and its interactions with other signaling factors in carcinoma cells.