gebhart/patrepeval huggingface dataset:
Electrical Activity of the Diaphragm during Pressure Support Ventilation in Acute Respiratory Failure (2001)

We compared crural diaphragm electrical activity (EAdi) with transdiaphragmatic pressure (Pdi) during varying levels of pressure support ventilation (PS) in 13 intubated patients. With changing PS, we found no evidence for changes in neuromechanical coupling of the diaphragm. From lowest to highest PS (2 cm H(2)O +/- 4 to 20 cm H(2)O +/- 7), tidal volume increased from 430 ml +/- 180 to 527 ml +/- 180 (p < 0.001). The inspiratory volume calculated during the period when EAdi increased to its peak did not change from 276 +/- 147 to 277 +/- 162 ml, p = 0.976. Respiratory rate decreased from 23.9 (+/- 7) to 21.3 (+/- 7) breaths/min (p = 0.015). EAdi and Pdi decreased proportionally by adding PS (r = 0.84 and r = 0.90, for mean and peak values, respectively). Mean and peak EAdi decreased (p < 0.001) by 33 +/- 21% (mean +/- SD) and 37 +/- 23% with the addition of 10 cm H(2)O of PS, similar to the decrease in the mean and peak Pdi (p < 0.001) observed (34 +/- 36 and 35 +/- 23%). We also found that ventilator assist continued during the diaphragm deactivation period, a phenomenon that was further exaggerated at higher PS levels. We conclude that EAdi is a valid measurement of neural drive to the diaphragm in acute respiratory failure.
Post-silicon bug diagnosis with inconsistent executions (2011)

The complexity of modern chips intensifies verification challenges, and an increasing share of this verification effort is shouldered by post-silicon validation. Focusing on the first silicon prototypes, post-silicon validation poses critical new challenges such as intermittent failures, where multiple executions of a same test do not yield a consistent outcome. These are often due to on-chip asynchronous events and electrical effects, leading to extremely time-consuming, if not unachievable, bug diagnosis and debugging processes. In this work, we propose a methodology called BPS (Bug Positioning System) to support the automatic diagnosis of these difficult bugs. During post-silicon validation, lightweight BPS hardware logs a compact encoding of observed signal activity over multiple executions of the same test: some passing, some failing. Leveraging a novel post-analysis algorithm, BPS uses the logged activity to diagnose the bug, identifying the approximate manifestation time and critical design signals. We found experimentally that BPS can localize most bugs down to the exact root signal and within about 1,000 clock cycles of their occurrence.
Identification of NAD-Dependent Xylitol Dehydrogenase from <i>Gluconobacter oxydans</i> WSH-003 (2019)

<i>Gluconobacter oxydans</i> plays an important role in the conversion of d-sorbitol to l-sorbose, which is an essential intermediate for the industrial-scale production of vitamin C. In the fermentation process, some d-sorbitol could be converted to d-fructose and other byproducts by uncertain dehydrogenases. Genome sequencing has revealed the presence of diverse genes encoding dehydrogenases in <i>G. oxydans</i>. However, the characteristics of most of these dehydrogenases remain unclear. Therefore, the analyses of these unknown dehydrogenases could be useful for identifying those related to the production of d-fructose and other byproducts. Accordingly, dehydrogenases in <i>G. oxydans</i> WSH-003, an industrial strain used for vitamin C production, were examined. A nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenase, which was annotated as xylitol dehydrogenase 2, was identified, codon-optimized, and expressed in <i>Escherichia coli</i> BL21 (DE3) cells. The enzyme exhibited a high preference for NAD<sup>+</sup> as the cofactor, while no activity with nicotinamide adenine dinucleotide phosphate, flavin adenine dinucleotide, or pyrroloquinoline quinone was noted. Although this enzyme presented high similarity with NAD-dependent xylitol dehydrogenase, it showed high activity to catalyze d-sorbitol to d-fructose. Unlike the optimum temperature and pH for most of the known NAD-dependent xylitol dehydrogenases (30-40 °C and about 6-8, respectively), those for the identified enzyme were 57 °C and 12, respectively. The values of <i>K</i> <sub>m</sub> and <i>V</i> <sub>max</sub> of the identified dehydrogenase toward l-sorbitol were 4.92 μM and 196.08 μM/min, respectively. Thus, xylitol dehydrogenase 2 can be useful for the cofactor-reduced nicotinamide adenine dinucleotide regeneration under alkaline conditions, or its knockout can improve the conversion ratio of d-sorbitol to l-sorbose.
Flow Characteristics of Soybean Constituents Controlled by Ratio of Total to Imbibed Water (1983)

ABSTRACT The objective was to quantify the relationship between water imbibing capacity of soybean components and their rheological characteristics in suspension. These components were: full fat soy flour, desludged full fat soy flour, defatted soy flour, soybean cell wall material and soybean sodium proteinate. It was found that the relationship between the ratio of the total to imbibed water (T/I) and consistency coefficient for all components at all concentrations could be expressed by a single curve. Flow behavior index vs T/I for all components also showed a single curve. A plot of apparent viscosity against T/I at the maximum shear rate showed that the data for all components at all concentrations fell on the same curve at a given shear rate.
Purification and analysis of the antigenicity of a 69000 Da protein from Bordetella pertussis (1990)

A purification scheme was devised for a 69-kDa outer membrane protein of Bordetella pertussis, a virulence-associated protein which may play a role in the pathogenesis of the organism. The protein was purified to apparent homogeneity by heating B. pertussis cells for 1 h at 60 degrees C followed by DEAE-Sepharose and Affi-Gel Blue chromatography. Antibodies found in sera obtained from patients diagnosed as having pertussis reacted with this protein. This purification scheme should be useful for the production of the 69 kDa protein which is currently being evaluated as a pertussis vaccine candidate.
A monoclonal antibody reactive with a 15-kDa cytoplasmic granule-associated protein defines a subpopulation of CD8+ T lymphocytes. (1990)

We have recently described a novel method for the production and characterization of mAb reactive with T cell-restricted intracellular antigens. From a panel of antibodies that react specifically with permeabilized T lymphocytes but not with permeabilized B lymphocytes or native T cells, we have selected one, designated TIA-1, that reacts with 20 to 36% of digitonin permeabilized peripheral blood T lymphocytes. Flow cytometric analysis of purified CD4+ and CD8+ subsets showed TIA-1 to recognize a subpopulation of 49 to 64% of CD8+ lymphocytes. Little or no reactivity with CD4+ resting T lymphocytes was observed. TIA-1 did not react with any of a panel of T cell lines, B cell lines, or monocytoid cell lines. TIA-1 reacted strongly with NK cell clones and CD8+ cytolytic T cell clones, and less strongly with CD4+-activated T cell clones, suggesting a preferential expression in cells possessing cytolytic potential. Cell fractionation experiments showed TIA-1 to be membrane associated. Furthermore, Percoll gradient fractionation of a cytolytic T cell clone (T4T8C1) showed the majority of TIA-1 to be contained in a low density membrane fraction that also contained serine protease activity. Immunoelectron microscopy showed TIA-1 to decorate the membranes of electron lucent and electron dense cytoplasmic granules in this same cytolytic T cell clone. Biochemical analysis showed TIA-1 to be a 15-kDa protein in unstimulated T cells. Upon activation with Con A or anti-CD3 antibodies. TIA-1 was induced to form disulfide linked dimers, trimers, and tetramers of the basic 15-kDa unit. Taken together, our data suggest that TIA-1 is a cytolytic granule associated protein that may define a subpopulation of resting CD8+ T lymphocytes possessing cytolytic potential.
Deep Reinforcement Learning for Robotic Manipulation with Asynchronous Off-Policy Updates (2016)

Reinforcement learning holds the promise of enabling autonomous robots to learn large repertoires of behavioral skills with minimal human intervention. However, robotic applications of reinforcement learning often compromise the autonomy of the learning process in favor of achieving training times that are practical for real physical systems. This typically involves introducing hand-engineered policy representations and human-supplied demonstrations. Deep reinforcement learning alleviates this limitation by training general-purpose neural network policies, but applications of direct deep reinforcement learning algorithms have so far been restricted to simulated settings and relatively simple tasks, due to their apparent high sample complexity. In this paper, we demonstrate that a recent deep reinforcement learning algorithm based on off-policy training of deep Q-functions can scale to complex 3D manipulation tasks and can learn deep neural network policies efficiently enough to train on real physical robots. We demonstrate that the training times can be further reduced by parallelizing the algorithm across multiple robots which pool their policy updates asynchronously. Our experimental evaluation shows that our method can learn a variety of 3D manipulation skills in simulation and a complex door opening skill on real robots without any prior demonstrations or manually designed representations.
Synthesis and characterization of a series of nickel(<scp>ii</scp>) alkoxide precursors and their utility for Ni(0) nanoparticle production (2017)

A series of nickel(ii) aryloxide ([Ni(OAr)<sub>2</sub>(py)<sub>x</sub>]) precursors was synthesized from an amide-alcohol exchange using [Ni(NR<sub>2</sub>)<sub>2</sub>] in the presence of pyridine (py). The H-OAr selected were the mono- and di-ortho-substituted 2-alkyl phenols: alkyl = methyl (H-oMP), iso-propyl (H-oPP), tert-butyl (H-oBP) and 2,6-di-alkyl phenols (alkyl = di-iso-propyl (H-DIP), di-tert-butyl (H-DBP), di-phenyl (H-DPhP)). The crystalline products were solved as solvated monomers and structurally characterized as [Ni(OAr)<sub>2</sub>(py)<sub>x</sub>], where x = 4: OAr = oMP (1), oPP (2); x = 3: OAr = oBP (3), DIP (4); x = 2: OAr = DBP (5), DPhP (6). The excited states (singlet or triplet) and various geometries of 1-6 were identified by experimental UV-vis and verified by computational modeling. Magnetic susceptibility of the representative compound 4 was fit to a Curie Weiss model that yielded a magnetic moment of 4.38(3)μ<sub>B</sub> consistent with a Ni<sup>2+</sup> center. Compounds 1 and 6 were selected for decomposition studied under solution precipitation routes since they represent the two extremes of coordination. The particle size and crystalline structure were characterized using transmission electron microscopy (TEM) and powder X-ray diffraction (PXRD). The materials isolated from 1 and 6 were found by TEM to form irregular shape nanomaterials (8-15 nm), which by PXRD were found to be Ni<sup>0</sup> hcp (PDF: 01-089-7129) and fcc (PDF: 01-070-0989), respectively.
Synthesis of Glycoconjugate Vaccines for <i>Candida </i><i>a</i><i>lbicans</i> Using Novel Linker Methodology (2005)

[reaction: see text] The cell wall phosphomannan of Candida species is a complex N-linked glycoprotein with a glycan chain that contains predominantly alpha-linked mannose residues. However, it is the minor beta-mannan component of the phosphomannan of clinically important Candida strains that provides immunological protection in animal models of fungal disease and hence holds promise as a component of conjugate vaccines. This important antigen occurs in different forms linked to the alpha-mannan backbone via a phosphodiester bond (acid-labile beta-mannan) or directly via a glycosidic bond. To reproducibly synthesize and evaluate conjugate vaccines, a robust method for the synthesis of the different oligosaccharide epitopes is required. Here, we report the gram-scale syntheses of both types of epitopes by an approach that utilizes glucosyl trichloroacetimidate donor 2 to first create a beta-glucopyranoside linkage and then epimerizes the C-2 center via an oxidation-reduction sequence that provides an efficient multigram scale route to the beta-mannopyranosides 5, 8, and 15. Reaction of glycosides 16-18 with homobifunctional adipic acid p-nitrophenyl diesters in dry DMF gave the corresponding half esters in good yields, and of sufficient stability to permit chromatographic purification. Subsequent conjugation with BSA and tetanus toxiod (TT) under mild conjugation conditions afforded the corresponding tri- and tetrasaccharide neoglycoproteins with good efficiency. The conjugation method is also applicable to the coupling of small amounts (mg) of larger oligosaccharides with different proteins.
Design and application of compliant quasi-kinematic couplings (2000)

A quasi-kinematic coupling for mating components (mechanical parts, surfaces, assem- blies and the like) employing mating sets of surface of revolution, (conical) grooves and cooperative surface of revolution (spherical/conical) protrusions for establishing six lines (not just prior points) of contact at the kinematic interfaces, and with elastic compliance therebetween and preferably with relief features to define the effective orientation as a clamping force seats the protrusions in the grooves and seals the component mating sur- faces into contact.
PPG Sensor and Device for Continuous Mobile Human Vital Signs Monitoring (2014)

We present a novel PPG optical sensor and device with ambient optical, electrical and electromagnetic noises cancellation, thus allowing only the useful optical signals to be received by health monitoring device. Sensor and methodology has been integrated into a prototype standalone device for noninvasive, continuous, wearable, remote and mobile monitoring of blood pressure and other human vital signs, such as heart rate, oxygen saturation, respiration rate, etc. This small device allows the user to read, store, process and transmit all the measurements to a remote location.
Novel Dual Repressor Elements for Neuronal Cell-specific Transcription of the Rat 5-HT1A Receptor Gene (2000)

The level of expression of the 5-HT1A receptor in the raphe and limbic systems is implicated in the etiology and treatment of major depression and anxiety disorders. The rat 5-HT1A receptor gene is regulated by a proximal TATA-driven promoter and by upstream repressors that inhibit gene expression. Deletion of a 71-base pair (bp) segment between -1590/-1519 bp of the 5-HT1A receptor gene induced over 10-fold enhancement of transcriptional activity in both 5-HT1A receptor-expressing (RN46A raphe and SN48 septal) cells and receptor-negative (L6 myoblast and C6 glioma) cells. A 31-bp segment of the repressor was protected from DNase I digestion by RN46A or L6 nuclear extracts. Within the 31-bp segment, a single protein complex was present in receptor-expressing cells that bound a novel 14-bp DNA element; in receptor-negative cells, an additional complex bound an adjacent 12-bp sequence. In receptor-positive but not receptor-negative cells, mutation of the 14-bp element to eliminate protein binding abrogated repression to nearly the same extent as deletion of the -1590/-1519 bp segment. Additional mutation of both 14-bp and 12-bp elements abolished protein binding and repressor activity in receptor-negative cells. Thus a single protein-DNA complex at the 14-bp element represses the 5-HT1A receptor gene in 5-HT1A receptor-positive neuronal cells, whereas adjacent DNA elements provide a dual repression mechanism in 5-HT1A receptor-negative cells.
Quartz Enhanced Photoacoustic Spectroscopy: Today and Beyond (2010)

Current theoretical understanding and practical applications of the trace gas sensing technique called quartz enhanced photoacoustic spectroscopy (QEPAS) will be presented. Work in progress and planned QEPAS developments will be discussed.
Radiolabeled B9958 Derivatives for Imaging Bradykinin B1 Receptor Expression with Positron Emission Tomography: Effect of the Radiolabel–Chelator Complex on Biodistribution and Tumor Uptake (2016)

Bradykinin B1 receptor (B1R), which is upregulated in a variety of malignancies, is an attractive cancer imaging biomarker. In this study we optimized the selection of radiolabel-chelator complex to improve tumor uptake and tumor-to-background contrast of radiolabeled analogues of B9958 (Lys-Lys-Arg-Pro-Hyp-Gly-Cpg-Ser-d-Tic-Cpg), a potent B1R antagonist. Peptide sequences were assembled on solid phase. Cold standards were prepared by incubating DOTA-/NODA-conjugated peptides with GaCl3, and by incubating AlOH-NODA-conjugated peptide with NaF. Binding affinities were measured via in vitro competition binding assays. (68)Ga and (18)F labeling experiments were performed in acidic buffer and purified by HPLC. Imaging/biodistribution studies were performed in mice bearing both B1R-positive (B1R+) HEK293T::hB1R and B1R-negative (B1R-) HEK293T tumors. Z02176 (Ga-DOTA-Pip-B9958; Pip: 4-amino-(1-carboxymethyl)piperidine), Z02137 (Ga-NODA-Mpaa-Pip-B9958; Mpaa: 4-methylphenylacetic acid), and Z04139 (AlF-NODA-Mpaa-Pip-B9958) bound hB1R with high affinity (Ki = 1.4-2.5 nM). (68)Ga-/(18)F-labeled peptides were obtained on average in ≥32% decay-corrected radiochemical yield with >99% radiochemical purity and 100-261 GBq/μmol specific activity. Biodistribution/imaging studies at 1 h postinjection showed that all tracers cleared rapidly from background tissues (except kidneys) and were excreted predominantly via the renal pathway. Only kidneys, bladders, and B1R+ tumors were clearly visualized in PET images. Uptake in B1R+ tumor was higher by using (68)Ga-Z02176 (28.9 ± 6.21 %ID/g) and (18)F-Z04139 (22.6 ± 3.41 %ID/g) than (68)Ga-Z02137 (14.0 ± 4.86 %ID/g). The B1R+ tumor-to-blood and B1R+ tumor-to-muscle contrast ratios were also higher for (68)Ga-Z02176 (56.1 ± 17.3 and 167 ± 57.6) and (18)F-Z04139 (58.0 ± 20.9 and 173 ± 42.9) than (68)Ga-Z02137 (34.3 ± 15.2 and 103 ± 30.2). With improved target-to-background contrast (68)Ga-Z02176 and (18)F-Z04139 are promising for imaging B1R expression in cancers with PET.
Analogues of Methotrexate in Rheumatoid Arthritis. 2. Effects of 5-Deazaaminopterin, 5,10-Dideazaaminopterin, and Analogues on Type II Collagen-Induced Arthritis in Mice (1997)

Twenty-six compounds derived from the 5-deaza- and 5,10-dideazaaminopterin series of aminopterin analogues were evaluated for antiarthritic activity in the mouse type II collagen model. New compounds in the 5-deaza series were prepared by alkylation of an appropriate N-substituted (4-aminobenzoyl)-L-glutamic acid dialkyl ester or N-(5-amino-2-thenoyl)-L-glutamate diester with a 2,4-diamino-5-alkyl-6-(bromomethyl)-5-deazapteridine. The resultant 5-deazaaminopterin diesters were saponified to provide the target 5-deaza analogues. 5,10-Dideazaaminopterins were synthesized by similar alkylation of the carbanions of appropriate 4-carboxyphenylacetic, (5-carboxy-2-thienyl)acetic, or (5-carboxy-2-pyridyl)acetic acid dimethyl esters. The diesters of the 2,4-diamino-4-deoxy-10-carboxy-5,10-dideazapteroic acid types so obtained were saponified and then readily decarboxylated by heating in Me2SO solution to provide the 2,4-diamino-5,10-dideazapteroic acid-type intermediates. Peptide coupling with diethyl L-glutamate followed by ester hydrolysis at room temperature afforded the new 5,10-dideazaaminopterin analogues. 5-Deazaaminopterins bearing an alkyl substituent at the 5-position were generally quite effective as antiinflammatory agents. Thus 5-propyl-5-deazaaminopterin, 5-methyl-10-propargyl-5-deazaaminopterin, 5-methyl-10-allyl-5-deazaaminopterin, 5-ethyl-5-deazamethotrexate, and 2,5-disubstituted thiophene analogue of 5-methyl-5-deazaaminopterin showed potencies greater than methotrexate by intraperitoneal or oral administration and were active over a considerably broader dose range. Useful activity in the 5,10-dideaza series was only observed for 5,10-dideazaaminopterin and its 10-methyl analogue. Alkyl substitution at C-5 or C-10 was generally detrimental to antiinflammatory activity in this series.
Joint detection and localization of multiple anatomical landmarks through learning (2008)

Reliable landmark detection in medical images provides the essential groundwork for successful automation of various open problems such as localization, segmentation, and registration of anatomical structures. In this paper, we present a learning-based system to jointly detect (is it there?) and localize (where?) multiple anatomical landmarks in medical images. The contributions of this work exist in two aspects. First, this method takes the advantage from the learning scenario that is able to automatically extract the most distinctive features for multi-landmark detection. Therefore, it is easily adaptable to detect arbitrary landmarks in various kinds of imaging modalities, e.g., CT, MRI and PET. Second, the use of multi-class/cascaded classifier architecture in different phases of the detection stage combined with robust features that are highly efficient in terms of computation time enables a seemingly real time performance, with very high localization accuracy. This method is validated on CT scans of different body sections, e.g., whole body scans, chest scans and abdominal scans. Aside from improved robustness (due to the exploitation of spatial correlations), it gains a run time efficiency in landmark detection. It also shows good scalability performance under increasing number of landmarks.
Gene Proximity Analysis across Whole Genomes via PQ Trees <sup>1</sup> (2005)

Permutations on strings representing gene clusters on genomes have been studied earlier by Uno and Yagiura (2000), Heber and Stoye (2001), Bergeron et al. (2002), Eres et al. (2003), and Schmidt and Stoye (2004) and the idea of a maximal permutation pattern was introduced by Eres et al. (2003). In this paper, we present a new tool for representation and detection of gene clusters in multiple genomes, using PQ trees (Booth and Leuker, 1976): this describes the inner structure and the relations between clusters succinctly, aids in filtering meaningful from apparently meaningless clusters, and also gives a natural and meaningful way of visualizing complex clusters. We identify a minimal consensus PQ tree and prove that it is equivalent to a maximal pi pattern (Eres et al., 2003) and each subgraph of the PQ tree corresponds to a nonmaximal permutation pattern. We present a general scheme to handle multiplicity in permutations and also give a linear time algorithm to construct the minimal consensus PQ tree. Further, we demonstrate the results on whole genome datasets. In our analysis of the whole genomes of human and rat, we found about 1.5 million common gene clusters but only about 500 minimal consensus PQ trees, with E. Coli K-12 and B. Subtilis genomes, we found only about 450 minimal consensus PQ trees out of about 15,000 gene clusters, and when comparing eight different Chloroplast genomes, we found only 77 minimal consensus PQ trees out of about 6,700 gene clusters. Further, we show specific instances of functionally related genes in two of the cases.