gebhart/patrepeval huggingface dataset:
Rhenium Tricarbonyl Core Complexes of Thymidine and Uridine Derivatives (2005)

Thymidine and uridine were modified at the C2' and C5' ribose positions to form amine analogues of the nucleosides (1 and 4). Direct amination with NaBH(OAc)3 in DCE with the appropriate aldehydes yielded 1-{5-[(bis(pyridin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L1), 1-{5-[(bis(quinolin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L2), and 1-[3-(bis(pyridin-2-ylmethyl)amino)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1H-pyrimidine-2,4-dione (L5), while standard coupling procedures of 1 and 4 with 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid (2) and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid (3) in the presence of HOBT-EDCI in DMF provided a second novel series of bifunctional chelators: 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L3), 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L4), 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L6), and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L7). The rhenium tricarbonyl complexes of L1-L4, L6, and L7, [Re(CO)3(LX)]Br (X=1-4, 6, 7: compounds 5-10, respectively), have been prepared by reacting the appropriate ligand with [NEt4][Re(CO)3Br3] in methanol. The ligands and their rhenium complexes were obtained in good yields and characterized by common spectroscopic techniques including 1D and 2D NMR, HRMS, IR, cyclic voltammetry, UV, and luminescence spectroscopy and X-ray crystallography. The crystal structure of complex 6.0.5NaPF6 displays a facial geometry of the carbonyl ligands. The nitrogen donors of the tridentate ligand complete the distorted octahedral spheres of the complex. Crystal data: monoclinic, C2, a = 24.618(3) A, b = 11.4787(11) A, c = 15.5902(15) A, beta = 112.422(4) degrees , Z = 4, D(calc) = 1.562 g/cm3.
A compact optical active connector: an optical interconnect module with an electrical connector interface (1999)

This paper describes a compact optical active connector that has both optical and electrical interfaces for an asynchronous-transfer-mode (ATM) switching system and high-speed computer network systems. This connector with an O/E or E/O conversion module can replace the conventional electrical-cable six-pin connector for an ordinary printed circuit board that has only an electrical interface. Our connector consists of a specially developed duplex MU-type submodule with photonic devices, an electrical connector, and integrated circuits (ICs). It can be used for 620-Mbps data transmission and has lower electromagnetic radiation noise than conventional connectors. Using optical active connectors to replace electrical-cable connectors will facilitate the introduction of high-throughput, large-capacity ATM switching systems, and next-generation local area network systems.
Constitutive activation of Stat3 signaling pathway in human colorectal carcinoma (2004)

Constitutive activation of Stat3 may play an important role in the tumorigenesis of colorectal carcinoma, and the detailed mechanism of Stat3 signaling pathway in CRC deserves further investigation.
Levels of DNA Polymorphism Vary With Mating System in the Nematode Genus Caenorhabditis (2002)

Self-fertilizing species often harbor less genetic variation than cross-fertilizing species, and at least four different models have been proposed to explain this trend. To investigate further the relationship between mating system and genetic variation, levels of DNA sequence polymorphism were compared among three closely related species in the genus Caenorhabditis: two self-fertilizing species, Caenorhabditis elegans and C. briggsae, and one cross-fertilizing species, C. remanei. As expected, estimates of silent site nucleotide diversity were lower in the two self-fertilizing species. For the mitochondrial genome, diversity in the selfing species averaged 42% of diversity in C. remanei. Interestingly, the reduction in genetic variation was much greater for the nuclear than for the mitochondrial genome. For two nuclear genes, diversity in the selfing species averaged 6 and 13% of diversity in C. remanei. We argue that either population bottlenecks or the repeated action of natural selection, coupled with high levels of selfing, are likely to explain the observed reductions in species-wide genetic diversity.
Capturing Inhalation Efficiency with Acoustic Sensors in Mobile Phones (2018)

Increasing popularity of inhaled therapy for the treatment of asthma and chronic obstructive pulmonary disease (COPD) stimulates research on both drug formulations and smart devices to support efficient pulmonary drug delivery. A major concern is the variability of the drug dose delivered to the lungs from the inhalation devices, due to the following three factors: 1) the drug formulation, 2) the device design, and 3) the patient's inhalation profile [23]. This paper investigates the use of microphones embedded in modern smartphones to accurately monitor the patient's inhalation manouvre. In our experiments we focus on dry powder inhalers (DPIs) with a breath-activated capsule spinning mechanism, such as Breezhaler®. We design an algorithm to capture inhalation profiles and evaluate it against measurements obtained with a precise gas flow meter. Our algorithm achieves an average error of up to 4.89 slm (standard liters per minute) given typical inspiratory flow rates through a Breezhaler® between 60 and 130 slm. We detect capsule rotation to ensure the inhalation was effective, and observe that the capsule spinning mechanism helps reduce measurement errors by 2 slm. Given a proper calibration, the proposed algorithm can be used with other capsule-based DPIs, such as HandiHaler®.
alpha-Fetoprotein-specific tumor immunity induced by plasmid prime-adenovirus boost genetic vaccination. (2001)

alpha-Fetoprotein (AFP) is a potential target for immunotherapy in hepatocellular carcinoma; both the murine and human T-cell repertoires can recognize AFP-derived epitopes in the context of the MHC. Protective immunity can be generated with AFP-engineered dendritic cell-based vaccines. We now report a DNA-based immunization strategy using a prime-boost approach: coadministration of plasmid DNA encoding murine AFP and murine granulocyte-macrophage colony-stimulating factor followed by boosting with an AFP-expressing nonreplicating adenoviral vector. This immunization strategy can elicit a high frequency of Th1-type AFP-specific cells leading to tumor protective immunity in mice at levels comparable with AFP-engineered dendritic cells. This cell-free mode of immunization is better suited for large-scale vaccine efforts for patients with hepatocellular carcinoma.
A real-time sub-carrier allocation scheme for multiple access downlink OFDM transmission (2005)

In this paper, we propose sub-carrier allocation algorithms for a multiple access scheme in downlink OFDM transmission. Knowing the channel characteristics of all the users at the base station, the sub-carrier allocation algorithm assigns sub-carriers to the users in a way that the total transmit power is minimized. An optimal algorithm is presented to provide the best sub-carrier assignment. The complexity of the optimal solution renders it impractical for real-time application. To deal with the frequently changing channel characteristic of a fast time-varying multipath fading channel, a heuristic algorithm based on constructive assignment and iterative improvement is proposed which can give out a valid solution in real time. Experimental results show that the performance of this real-time algorithm is close to that of the optimal allocation.
Seismic Retrofit with Continuous Slurry-Infiltrated Mat Concrete Jackets (2003)

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Construction of a Proline-Producing Mutant of the Extremely Thermophilic Eubacterium Thermus thermophilus HB27 (1998)

Growth of Thermus thermophilus HB27 was inhibited by a proline analog, 3,4-dehydroproline (DHP). This result suggested that the gamma-glutamyl kinase (the product of the proB gene) was inhibited by feedback inhibition in T. thermophilus. DHP-resistant mutants were reported previously for Escherichia coli (A. M. Dandekar and S. L. Uratsu, J. Bacteriol. 170:5943-5945, 1988) and Serratia marcescens (K. Omori, S. Suzuki, Y. Imai, and S. Komatsubara, J. Gen. Microbiol. 138:693-699, 1992), and their mutated sites in the proB gene were identified. Comparison of the amino acid sequence of T. thermophilus gamma-glutamyl kinase with those of E. coli and S. marcescens mutants revealed that the DHP resistance mutations occurred in the amino acids conserved among the three organisms. For eliminating the feedback inhibition, we first constructed a DHP-resistant mutant, TH401, by site-directed mutagenesis at the proB gene as reported for the proline-producing mutant of S. marcescens. The mutant, TH401, excreted about 1 mg of L-proline per liter at 70 degreesC after 12 h of incubation. It was also suggested that T. thermophilus had a proline degradation and transport pathway since it was able to grow in minimal medium containing L-proline as sole nitrogen source. In order to disrupt the proline degradation or transport genes, TH401 was mutated by UV irradiation. Seven mutants unable to utilize L-proline for their growth were isolated. One of the mutants, TH4017, excreted about 2 mg of L-proline per liter in minimal medium at 70 degreesC after 12 h of incubation.
Mode-selective photonic lanterns for space-division multiplexing (2014)

We demonstrate a 3x1 fiber-based photonic lantern spatial-multiplexer with mode-selectivity greater than 6 dB and transmission loss of less than 0.3 dB. The total insertion loss of the mode-selective multiplexers when coupled to a graded-index few-mode fiber was < 2 dB. These mode multiplexers showed mode-dependent loss below 0.5 dB. To our knowledge these are the lowest insertion and mode-dependent loss devices, which are also fully compatible with conventional few-mode fiber technology and broadband operation.
Listeria-based vaccines for cancer treatment. (2005)

Listeria monocytogenes is a facultative intracellular bacterium that enters professional antigen-presenting cells by active phagocytosis. As a live bacterium, it induces antigen-presenting cell maturation and strong innate immunity which may assist in the immune response to poorly immunogenic antigens, such as tumor-associated antigens. Listeria produces virulence factors that allow it to escape from the phagolysosome and colonize the cytosol of the host cell. It is thus a potent vaccine vector for the presentation of passenger antigens to the major histocompatibility complex class I and II pathways of antigen processing and presentation. Recent progress in developing this bacterium as a vaccine vector for tumor-associated antigens is reviewed. In mouse models, recombinant Listeria carrying a number of such antigens has provided therapeutic immunity directed towards established tumors. Safety issues associated with live bacterial vaccine vectors and problems to be overcome in developing Listeria as a cancer immunotherapeutic for human use are also discussed.
Use of Gabapentin in Pain Management (1997)

There have been many proposed uses for gabapentin, including midscapular pain secondary to radiation myelopathy, RSD, neuropathic pain, postherpetic neuralgia, and migraine prophylaxis. However, the published reports consist of a small number of patients and limited data. Limited data provided in published case reports do not allow adequate evaluation of expected adverse effects or efficacy. It is unclear whether gabapentin is more effective for a specific type of pain and how gabapentin may compare with placebo or other therapeutic alternatives. Therefore, randomized, double-blind, placebo-controlled, prospective studies are warranted to further elucidate gabapentin uses beyond what is recommended by the Food and Drug Administration. Gabapentin should only be considered for pain management after well-established therapies have failed to produce desired outcomes.
Fetuin-A Regulation of Calcified Matrix Metabolism (2011)

The final step of biomineralization is a chemical precipitation reaction that occurs spontaneously in supersaturated or metastable salt solutions. Genetic programs direct precursor cells into a mineralization-competent state in physiological bone formation (osteogenesis) and in pathological mineralization (ectopic mineralization or calcification). Therefore, all tissues not meant to mineralize must be actively protected against chance precipitation of mineral. Fetuin-A is a liver-derived blood protein that acts as a potent inhibitor of ectopic mineralization. Monomeric fetuin-A protein binds small clusters of calcium and phosphate. This interaction results in the formation of prenucleation cluster-laden fetuin-A monomers, calciprotein monomers, and considerably larger aggregates of protein and mineral calciprotein particles. Both monomeric and aggregate forms of fetuin-A mineral accrue acidic plasma protein including albumin, thus stabilizing supersaturated and metastable mineral ion solutions as colloids. Hence, fetuin-A is a mineral carrier protein and a systemic inhibitor of pathological mineralization complementing local inhibitors that act in a cell-restricted or tissue-restricted fashion. Fetuin-A deficiency is associated with soft tissue calcification in mice and humans.
Analysis and simulation of a neutralizing epitope of transmissible gastroenteritis virus (1990)

The amino acid sequences recognized by monoclonal antibodies (MAbs) specific for the antigenic site IV of the spike protein S of transmissible gastroenteritis virus were analyzed by PEPSCAN. All MAbs of group IV recognized peptides from the S region consisting of residues 378 to 390. In addition, the neutralizing MAbs (subgroup IV-A) also bound to peptides from the region consisting of residues 1173 to 1184 and to several other peptides with a related amino acid composition. The contribution of the individual residues of both sequences to the binding of a MAb was determined by varying the length of the peptide and by a consecutive deletion or replacement of parental residues by the 19 other amino acids. The sequence consisting of residues 326 to 558, tested as part of a cro-beta-galactosidase hybrid protein, was antigenic, but the sequence consisting of residues 1150 to 1239 was not. Furthermore, antibodies raised in rabbits against the peptide SDSSFFSYGEIPFGN (residues 377 to 391), but not those raised against the peptide VRASRQLAKDKVNEC (residues 1171 to 1185), recognized the virus and had neutralizing activity. We infer that the epitope of the neutralizing MAbs is composite and consists of the linear sequence SFFSYGEI (residues 380 to 387) with contributions of A, D, K, N, Q, or V residues from other parts of the S molecule. The complex epitope was simulated by synthesizing peptides in which the sequences consisting of residues 380 to 387 and 1176 to 1184 were combined. MAbs of subgroup IV-A recognized the combination peptides two to six times better than the individual sequences. These results may offer prospects for the development of an experimental vaccine.
Commensal Akkermansia muciniphila Exacerbates Gut Inflammation in Salmonella Typhimurium-Infected Gnotobiotic Mice (2013)

Excessive mucin degradation by intestinal bacteria may contribute to inflammatory bowel diseases because access of luminal antigens to the intestinal immune system is facilitated. This study investigated how the presence of a mucin degrading commensal bacterium affects the severity of an intestinal Salmonella enterica Typhimurium-induced gut inflammation. Using a gnotobiotic C3H mouse model with a background microbiota of eight bacterial species (SIHUMI) the impact of the mucin-degrading commensal bacterium Akkermansia muciniphila (SIHUMI-A) on inflammatory and infectious symptoms caused by S. Typhimurium was investigated. Presence of A. muciniphila in S. Typhimurium-infected SIHUMI mice caused significantly increased histopathology scores and elevated mRNA levels of IFN-γ, IP-10, TNF-α, IL-12, IL-17 and IL-6 in cecal and colonic tissue. The increase in pro-inflammatory cytokines was accompanied by 10-fold higher S. Typhimurium cell numbers in mesenteric lymph nodes of SIHUMI mice associated with A. muciniphila and S. Typhimurium (SIHUMI-AS) compared to SIHUMI mice with S. Typhimurium only (SIHUMI-S). The number of mucin filled goblet cells was 2- to 3-fold lower in cecal tissue of SIHUMI-AS mice compared to SIHUMI-S, SIHUMI-A or SIHUMI mice. Reduced goblet cell numbers significantly correlated with increased IFN-γ mRNA levels (r(2) = -0.86, ***P<0.001) in all infected mice. In addition, loss of cecal mucin sulphation was observed in SIHUMI mice containing both A. muciniphila and S. Typhimurium compared to other mouse groups. Concomitant presence of A. muciniphila and S. Typhimurium resulted in a drastic change in microbiota composition of SIHUMI mice: the proportion of B. thetaiotaomicron in SIHUMI-AS mice was 0.02% of total bacteria compared to 78%-88% in the other mouse groups and the proportion of S. Typhimurium was 94% in SIHUMI-AS mice but only 2.2% in the SIHUMI-S mice. These results indicate that A. muciniphila exacerbates S. Typhimurium-induced intestinal inflammation by its ability to disturb host mucus homeostasis.
Interleukin-4 Enhances Pulmonary Clearance ofPseudomonas aeruginosa (1998)

To determine the effects of interleukin-4 (IL-4) on bacterial clearance from the mouse lung, transgenic mice expressing IL-4 in respiratory epithelial cells under the control of the Clara cell secretory protein promoter (CCSP-IL-4 mice) were infected intratracheally with Pseudomonas aeruginosa. Survival of CCSP-IL-4 mice following bacterial administration was markedly improved compared with that of control mice. While bacteria proliferated in lungs of wild-type mice, a rapid reduction in the number of bacteria was observed in the IL-4 mice as early as 6 h postinfection. Similarly, intranasal administration of IL-4 enhanced bacterial clearance from the lungs of wild-type mice. While acute and chronic IL-4 increased the numbers of neutrophils in bronchoalveolar lavage fluid, bacterial infection was associated with acute neutrophilic pulmonary infiltration, and this response was similar in the presence or absence of IL-4. Local administration or expression of IL-4 in the mouse lung enhanced pulmonary clearance of P. aeruginosa in vivo and decreased mortality following infection.
Use of a Medical Records Linkage System to Enumerate a Dynamic Population Over Time: The Rochester Epidemiology Project (2011)

The Rochester Epidemiology Project (REP) is a unique research infrastructure in which the medical records of virtually all persons residing in Olmsted County, Minnesota, for over 40 years have been linked and archived. In the present article, the authors describe how the REP links medical records from multiple health care institutions to specific individuals and how residency is confirmed over time. Additionally, the authors provide evidence for the validity of the REP Census enumeration. Between 1966 and 2008, 1,145,856 medical records were linked to 486,564 individuals in the REP. The REP Census was found to be valid when compared with a list of residents obtained from random digit dialing, a list of residents of nursing homes and senior citizen complexes, a commercial list of residents, and a manual review of records. In addition, the REP Census counts were comparable to those of 4 decennial US censuses (e.g., it included 104.1% of 1970 and 102.7% of 2000 census counts). The duration for which each person was captured in the system varied greatly by age and calendar year; however, the duration was typically substantial. Comprehensive medical records linkage systems like the REP can be used to maintain a continuously updated census and to provide an optimal sampling framework for epidemiologic studies.
T cell activation by purified, soluble, class I MHC molecules. Requirement for polyvalency. (1988)

To examine the nature of the interaction of the TCR with the MHC class I Ag, we have studied the stimulation requirements of an H-2Dd-reactive T cell hybridoma, using a homogeneous, purified preparation of a molecularly engineered soluble counterpart of the class I Ag, H-2Dd/Q10b. We demonstrate that this monovalent, soluble MHC Ag is incapable of stimulating the release of IL-2 from this T cell hybridoma. However, the same preparation of the purified protein can elicit a dose-dependent response when made multivalent either by covalent coupling to soluble, high m.w. dextran or to agarose beads, or by adsorption to polystyrene tissue culture plates.
Biodegradable Polyesters Derived from Amino Acids (2009)

New optically active polyesters derived from amino acids by replacement of the backbone amino groups for hydroxyl residues are presented. The polyesters described are the following: poly(L)HOAsp(COOH)−OH, poly(L)HOGlu(COOH)−OH, poly(L)HOSer(OH)−OH, poly(L)HOThr(OH)−OH, poly(L)HOLys(OH)−OH, and poly(HOAa(X)(OH)-co-LA) and some other copolymers of α-hydroxy acids. The polymers were prepared via (a) direct condensation in bulk employing several catalysts as PTSA, boric acid, Mukaiyama's reagent, stannous chloride dihydrate, (b) acyl halide activation, and (c) microwave-assisted polymerization. The obtained polymers reached a molecular weight between 1000 and 4000. The highest molecular weight attained employing polycondensation methods in solution, was either by utilizing polyacid, or metal catalyst (boric acid and stannous chloride respectively). Applying oxalyl chloride for chain extension also showed to be an efficient method. On the other hand, the microwave-assisted polymerization exhibited significant advantages and polymerization could be implemented with lack of solvent (neat). The polymers were characterized by several methods (GPC, CD, DSC, solubility), and tested for their degradability and biocompatibility to cell growth. Most of the polymers displayed a linear correlation between their calculated log P values and their experimental contact angles parameters. Transition glass temperatures (Tg) of copolymers with various compositions of LA were correlated to either Gordon Taylor equation or to a three parameters modified Kwei equation. The circular dichroism spectra (CD) of several homo and copolymers were measured. In general, CD curves of the homopolymers of HOSer, HOGlu, HOThr, HOAsp, and HOLys(OH) revealed a significant ester maxima approximately at 205−220 nm while the copolymers of HOSer with HOPhe displayed an additional cotton effect band at 200.6−201.5 nm. This is accounted for polymer rotational isomers and not to a different ππ* transition at lower wavelength.