gebhart/patrepeval huggingface dataset:
Quinolone antibacterials containing the new 7-[3-(1-aminoethyl)-1-pyrrolidinyl] side chain: the effects of the 1-aminoethyl moiety and its stereochemical configurations on potency and in vivo efficacy (1993)

A series of stereochemically pure 7-[3-(1-aminoethyl)-1-pyrrolidinyl]-1, 4-dihydro-4-oxoquinoline and 1,8-naphthyridine-3-carboxylic acids, with varied substituents at the 1-, 5-, and 8-positions, were synthesized to study the effects of the 7-[3-(1-aminoethyl)-1- pyrrolidinyl] moiety on potency and in vivo efficacy relative to the known 7-[3-(aminomethyl)-1- pyrrolidinyl] derivatives. The antibacterial efficacies of the target compounds and their relevant reference agents were determined in vitro using an assortment of Gram-negative and Gram-positive organisms and in vivo using Escherichia coli and Streptococcus pyogenes mouse infection models. The effects of the 7-[3-(1-aminoethyl)-1-pyrrolidinyl] moiety were also examined at the level of the target enzyme by employing a DNA-gyrase supercoiling inhibition assay. Selected compounds were further evaluated for potential phototoxic and clastogenic liabilities using a phototoxicity mouse model and an in vitro mammalian cell cytotoxicity assay. It was found that the differences in in vitro antibacterial activity between the stereoisomers were significantly greater than previously reported for other optically pure 3-substituted pyrrolidinyl side chains. Relative to their 7-[3-(aminomethyl)-1-pyrrolidinyl] analogs, the (3R,1S)-3-(1-aminoethyl)pyrrolidines generally conferred a 2-4-fold increase in Gram-positive in vitro activity and an average of 10-fold improvement in oral efficacy. The level of phototoxicity and cytotoxicity of the product quinolones was ultimately determined by the combined influence of the 7-[3-(1-aminoethyl)-1-pyrrolidinyl] side chains and the other quinolone substituents. From this study, several compounds were identified with outstanding antibacterial activity and low degrees of phototoxicity and mammalian cell cytotoxicity. One such agent, 34F-R,S (PD 140248), showed the best overall blend of safety and efficacy.
Early Severe Inflammatory Responses to Uropathogenic E. coli Predispose to Chronic and Recurrent Urinary Tract Infection (2010)

Chronic infections are an increasing problem due to the aging population and the increase in antibiotic resistant organisms. Therefore, understanding the host-pathogen interactions that result in chronic infection is of great importance. Here, we investigate the molecular basis of chronic bacterial cystitis. We establish that introduction of uropathogenic E. coli (UPEC) into the bladders of C3H mice results in two distinct disease outcomes: resolution of acute infection or development of chronic cystitis lasting months. The incidence of chronic cystitis is both host strain and infectious dose-dependent. Further, development of chronic cystitis is preceded by biomarkers of local and systemic acute inflammation at 24 hours post-infection, including severe pyuria and bladder inflammation with mucosal injury, and a distinct serum cytokine signature consisting of elevated IL-5, IL-6, G-CSF, and the IL-8 analog KC. Mice deficient in TLR4 signaling or lymphocytes lack these innate responses and are resistant, to varying degrees, to developing chronic cystitis. Treatment of C3H mice with the glucocorticoid anti-inflammatory drug dexamethasone prior to UPEC infection also suppresses the development of chronic cystitis. Finally, individuals with a history of chronic cystitis, lasting at least 14 days, are significantly more susceptible to redeveloping severe, chronic cystitis upon bacterial challenge. Thus, we have discovered that the development of chronic cystitis in C3H mice by UPEC is facilitated by severe acute inflammatory responses early in infection, which subsequently are predisposing to recurrent cystitis, an insidious problem in women. Overall, these results have significant implications for our understanding of how early host-pathogen interactions at the mucosal surface determines the fate of disease.
Evaluation of hip arthroprostheses by means of body environment simulators (1977)

Laboratory tests carried out by means of body environment simulators have proved to be very important for the evaluation of endoprostheses potentially useful for implantation. The present paper examines the problems connected with the design of such a simulator. The results obtained with an initial, very primitive simulator concerning the outlines of the phenomena of wear, corrosion, and friction and some wear properties of commercially available hip endoprostheses are presented. From these results, the motivation that led to the design of a more advanced simulator is presented. This latter simulator is also described.
Therapeutic Gain Factors for Fractionated Radiation Treatment of Spontaneous Murine Tumors Using Fast Neutrons, Photons Plus O 2 1 or 3 ATA, or Photons Plus Misonidazole (1988)

Therapeutic gain factors (TGFs) have been determined for three spontaneous tumors of the C3H mouse treated by photons + normobaric oxygen (O2(1) ATA), photons + hyperbaric oxygen (O2 3 ATA), photons + misonidazole, or fast neutrons. The tumors were early generation isotransplants of spontaneous tumors: MCaIV, a mammary carcinoma; FSaII, a fibrosarcoma; and SCCVII, a squamous cell carcinoma. The tumors, transplanted to the right leg, were 6 mm at start of treatment. Normal tissue responses studied were acute reaction of normal skin (all treatment modalities) and LD50 following irradiation of the upper abdomen (in test of photons + O2 at 1 or 3 ATA). Thus both the tumor and normal tissues would be classified as "acute responding." All subject tissues were at congruent to 34.5-35 degrees C at irradiation. Treatments were based on d(25)Be or p(43)Be fast neutron beams, 60Co and 137Cs photon beams. Treatments were given in 5 or 15 equal doses in 5 days. For photon treatments, TGFs (air/O2 3 ATA) were substantially and significantly larger than 1 for all three tumor systems treated at small or large doses per fraction when related to skin or abdominal tissue responses. The TGFs (air/O2 1 ATA) were greater than 1 at small doses per fraction for MCaIV and FSaII for skin as the normal tissue; the TGFs for all three tumors and at all doses per fraction would be greater than 1 when related to upper abdominal tissues. TGFs (O2 1 ATA/O2 3 ATA) for photon irradiation greater than 1 were found only for SCCVII and that obtained for both large and small doses per fraction. Misonidazole achieved impressive TGFs (air/air + miso or air/O2 1 ATA + miso); the drug was tested only at 10-12 Gy/fraction and relative to skin. RBEs(FN) for the three tumors were lower at 1.5-2 Gy(FN)/fraction than at 5-6 Gy(FN)/fraction, i.e. the opposite to that reported for normal tissue (RBE increases with decreasing dose per fraction). A TGF (relative to skin reaction) greater than 1 for fast neutron therapy was found only for SCCVII when treated at large doses/fraction; this was true for air or O2 1 ATA conditions.
Implementation and Characterization of a System for the Evaluation of the Starting Instant of Lightning-Induced Transients (2007)

Voltage transients are one of the main causes of power quality (PQ) degradation. There is a search for investigation techniques that are capable of characterizing and classifying them depending on their origin. A distributed measurement system for PQ monitoring can be used in parallel with a lightning location system (LLS) to assess whether a lightning event is responsible for a voltage transient. This involves the accurate estimate of the transient's starting instant. In this paper, a system for the measurement of the starting instant of voltage transients is described. It is hosted in each remote unit of a distributed system, which was built in our laboratory, for PQ monitoring. The results of the characterization tests are also reported and discussed. They lead us to conclude that our system for PQ monitoring can be used in parallel with an LLS to assess whether an impulsive voltage transient was induced by lightning.
Reply re (2014)

Biro, Nicolas M.D.; Murchison, Ann P. M.D., M.P.H.; Pribitkin, Edmund A. M.D.; Rosen, Marc R. M.D.; Bilyk, Jurij R. M.D. Author Information
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis (2006)

Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.
On the stability of linear dynamic systems on time scales (2008)

In this paper, we introduce u ∞-similarity in order to unify (continuous) t ∞-similarity and (discrete) n ∞-similarity and then investigate the strong stability for dynamic equations on time scales by using the concept of u ∞-similarity.
Chapter 3: Bowel Disorders (2017)

Diagnostic Algorithms for Common GI Symptoms 2ND Edition This page contains the DOI reference links for the online version of the Rome IV book, volumes I and II. If you have a Rome Online subscription and are logged in,
On the Capacity of a Class of Cognitive Z-interference Channels (2010)

We study a special class of the cognitive radio channel in which the receiver of the cognitive pair does not suffer interference from the primary user. Previously developed general encoding schemes for this channel are complex as they attempt to cope with arbitrary channel conditions, which leads to rate regions that are difficult to evaluate. The focus of our work is to derive simple rate regions that are easily computable, thereby providing more insights into achievable rates and good coding strategies under different channel conditions. We first present several explicit achievable regions for the general discrete memoryless case. We also present an improved outer bound on the capacity region for the case of high interference. We then extend these regions to Gaussian channels. With a simple outer bound we establish a new capacity region in the high-interference regime. Lastly, we provide numerical comparisons between the derived achievable rate regions and the outer bounds.
Speech and Speaker Recognition from Raw Waveform with SincNet (2018)

Deep neural networks can learn complex and abstract representations, that are progressively obtained by combining simpler ones. A recent trend in speech and speaker recognition consists in discovering these representations starting from raw audio samples directly. Differently from standard hand-crafted features such as MFCCs or FBANK, the raw waveform can potentially help neural networks discover better and more customized representations. The high-dimensional raw inputs, however, can make training significantly more challenging. This paper summarizes our recent efforts to develop a neural architecture that efficiently processes speech from audio waveforms. In particular, we propose SincNet, a novel Convolutional Neural Network (CNN) that encourages the first layer to discover meaningful filters by exploiting parametrized sinc functions. In contrast to standard CNNs, which learn all the elements of each filter, only low and high cutoff frequencies of band-pass filters are directly learned from data. This inductive bias offers a very compact way to derive a customized front-end, that only depends on some parameters with a clear physical meaning. Our experiments, conducted on both speaker and speech recognition, show that the proposed architecture converges faster, performs better, and is more computationally efficient than standard CNNs.
Limbic regions of the brain of Alzheimer's disease patients show selective changes in mu, delta and kappa opioid receptor binding. (1986)

Total opioid binding and levels of the three major types of opioid binding sites were measured in homogenates of various limbic structures from post-mortem brains of Alzheimer's Disease (AD) patients and age-matched control individuals. AD brains showed an increase in kappa binding in all six areas of the limbic system examined, with the putamen and caudate regions showing significant increases of 114% and 53%, respectively. In addition, the AD putamen showed a significantly higher level of total binding (85% increase). The amygdala of AD patients exhibited significantly lower levels of mu and delta binding (41% and 55% decrease, respectively).
Usefulness of HIV-1 V3 serotyping in studying the HIV-1 epidemic in South Africa. (1998)

In South Africa HIV-1 subtype B infection is associated with male homosexual transmission while infection with HIV-1 subtype C is associated with heterosexual transmission. 119 serum and plasma samples collected from HIV-1-infected individuals from three separate geographical regions in South Africa and for whom genetic subtypes were known were serotyped in a blinded manner. Study subjects included 26 heterosexual women and 25 homosexual 5 bisexual and 61 heterosexual men. The genetic subtypes of HIV-1 were determined by either heteroduplex mobility assay or env and gag sequence analysis. A good correlation was found between HIV-1 V3 serotypes B and C and the corresponding genetic subtypes. 23 (68%) of 34 subtype B sera were classified as serotype B and 74 (90%) of 82 subtype C sera were correctly classified as serotype C. Mismatches between serotype and genotype were observed in 3 subtype B samples while 2 subtype C samples were identified as serotype A or A/C. However all 23 serotype B samples belonged to genetic subtype B and 74 of 76 serotype C samples were genetic subtype C. 15 sera were nonreactive. V3 C serotype was present in all three regions and the most prevalent serotype in Bloemfontein and Westonaria while diverse V3 serotypes were observed in Cape Town. Study results suggest that HIV-1 serotyping can help in investigating HIV-1 distribution and routes of transmission in South Africa.
In Situ Phase Separation of NiAu Alloy Nanoparticles for Preparing Highly Active Au/NiO CO Oxidation Catalysts (2008)

Multifunctional catalysts: Nickel–gold alloy nanoparticles (NPs) are synthesized in solution, by means of a fast butyllithium reduction method, and then used to prepare NiO-stabilized Au NP catalysts through a phase-transformation process (see scheme). The silica-supported catalysts exhibit a remarkable resistance to sintering and are highly active for CO oxidation. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Effects of Irradiance and Stimulus Duration on Early Gene Expression (Fos) in the Suprachiasmatic Nucleus: Temporal Summation and Reciprocity (2000)

The daily behavioral, physiological, and hormonal rhythms in mammals are regulated by an endogenous circadian clock located in the suprachiasmatic nucleus (SCN) and are synchronized by the natural 24 hr light/dark cycle. We studied the response properties (threshold, saturation, and linearity) of the photic system to irradiance by assaying light induction of Fos, the protein product of the immediate early gene c-fos. Fos expression was quantified by image analysis in the SCN and in the retina. Fos expression in the SCN and retina are unrelated because the response differs in terms of threshold, saturation, and range. In the SCN, Fos expression increases proportionately to increases in both irradiance and duration of light exposure. The photic system shows a linear temporal integration of photons for durations ranging from 3 sec to 47.5 min. The principal result of this study shows that in the SCN, Fos expression is directly proportional to the total number of photons rather than to irradiance or duration alone (reciprocity), and that integration occurs over a range of 5 log units of photon number. This report provides the first demonstration that the mechanism of photon integration by the circadian system is expressed at a cellular level in the SCN.
Effect of Autumn Foliar Senescence on Chlorophyll a:b Ratio and Respiratory Enzymes of Populus tremuloides (1993)

Maria A. Dean, Charles A. Letner, James H. Eley, Effect of Autumn Foliar Senescence on Chlorophyll a:b Ratio and Respiratory Enzymes of Populus tremuloides, Bulletin of the Torrey Botanical Club, Vol. 120, No. 3 (Jul. - Sep., 1993), pp. 269-274
Distribution kinetics of polymer crystallization and the Avrami equation (2005)

Cluster distribution kinetics is adopted to explore the kinetics of polymer crystallization. Population balance equations based on crystal size distribution and concentration of amorphous polymer segments are solved numerically and the related dynamic moment equations are also solved. The model accounts for heterogeneous or homogeneous nucleation and crystal growth. Homogeneous nucleation rates follow the classical surface-energy nucleation theory. Different mass dependences of growth and dissociation rate coefficients are proposed to investigate the fundamental features of nucleation and crystal growth. A comparison of moment solutions with numerical solutions examines the validity of the model. The proposed distribution kinetics model provides a different interpretation of the familiar Avrami equation.
B-1 cells secrete antibodies with anti-tumor properties (2016)

Abstract It is well known that B-1 cells are the main B cell subset responsible for the production of natural antibodies. Several studies suggest that natural IgM antibodies play an important role in immunosurveillance against transformed cells in humans, preferentially binding glycolipids and carbohydrate structures. NeuGcGM3 ganglioside is a sialic acid containing glycosphingolipid that has been considered an attractive target for cancer immunotherapy since is not naturally expressed in healthy human tissues but is overexpressed in several tumors. We previously described the existence of cytotoxic anti-tumor antibodies against NeuGcGM3 ganglioside in healthy young subjects. However, whether this anti-tumor antibody response has a “natural origin” is unknown. With the present work we aimed to elucidate whether B-1 cells have the potential to secrete anti-NeuGcGM3 antibodies. First we generated four mouse monoclonal antibodies from Balb/c mouse peritoneal B cells. All hibridomas secreted IgM which bound NeuGcGM3 but no other gangliosides and recognized and killed NeuGcGM3 positive tumor cells. All the anti-NeuGcGM3 IgM-producing hybridomas were CD5+ B-1 cells. Then naïve, memory, plasma and B-1 cells were purified from healthy human donors PBMC and stimulated in vitro to produce immunoglobulins. All the B-1 cell supernatants reacted with NeuGcGM3 and most of them also recognized tumor cells expressing this ganglioside. Only 40% of memory samples, and none from naïve or plasma cells, recognized this antigen. These data suggest a protective role for B-1 cells against malignant cells through the production of natural antibodies reactive to tumor associated antigens such as NeuGcGM3 ganglioside.
Cell Atlases as Roadmaps in Health and Disease (2020)

The recent advent of methods for high-throughput single-cell and spatial profiling have opened the way to complete the 150-year-old endeavor of identifying all cell types in the human body, by their distinctive molecular profiles, and to relate this information to other cellular descriptions, physiological phenotypes, molecular mechanisms and functions. Our effort to build a comprehensive reference map of the molecular state of cells in healthy human tissues is propelling the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, provides a framework for understanding cellular dysregulation in human disease, and suggests the possibility of predicting cell types and behaviors, towards a "periodic table of our cells". In this talk, I describe our foundational work underlying single cell genomics and the conceptual framework and impact of our understanding of cell and tissue biology in health, as well as how we use it to shed light on rare disease, cancer, and COVID-19.
Automatic analyzer for highly polar carboxylic acids based on fluorescence derivatization–liquid chromatography (2014)

A sensitive, versatile, and reproducible automatic analyzer for highly polar carboxylic acids based on a fluorescence derivatization-liquid chromatography (LC) method was developed. In this method, carboxylic acids were automatically and fluorescently derivatized with 4-(N,N-dimethylaminosulfonyl)-7-piperazino-2,1,3-benzoxadiazole (DBD-PZ) in the presence of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride by adopting a pretreatment program installed in an LC autosampler. All of the DBD-PZ-carboxylic acid derivatives were separated on the ODS column within 30 min by gradient elution. The peak of DBD-PZ did not interfere with the separation and the quantification of all the acids with the exception of lactic acid. From the LC-MS/MS analysis, we confirmed that lactic acid was converted to an oxytriazinyl derivative, which was further modified with a dimethoxy triazine group of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM). We detected this oxytriazinyl derivative to quantify lactic acid. The detection limits (signal-to-noise ratio = 3) for the examined acids ranged from 0.19 to 1.1 µm, which correspond to 95-550 fmol per injection. The intra- and inter-day precisions of typical, highly polar carboxylic acids were all <9.0%. The developed method was successfully applied to the comprehensive analysis of carboxylic acids in various samples, which included fruit juices, red wine and media from cultured tumor cells.
Flow Characterization of an Electrostatic Resonant Plate Micropump-Mixer by a Scaled Model (2006)

Flow characterization of an electrostatically activated resonant-plate micropump-mixer was investigated. Detailed visualization of the mixing process at the tip of the resonant plate, which is almost impossible due to the high actuation frequency (10–30 kHz) and small scale of the resonant plate (250 micron) under normal conditions, was realized with a macro scale flow visualization experiment within the range of common visualization equipment such as a SLR camera. Flow phenomena such as distinct circulative regions, observed at the micro scale by Linderman et. al [1,2], were observed in this study. In addition, the transition between two different flow regimes was observed, corresponding to vortex shearing and vortex shedding respectively. This transition took place in a gradual manner over a range of Reynolds numbers between 20 and 98. Below this regime the resonant plate will only generate limited deformation of the interface between the two fluids. However, for larger Reynolds numbers, equivalent to higher plate frequencies, organized vortex roll-up is observed. Vortex roll-up indicates significant fluid entrainment, and consequently mixing. The visualization of the flow, generated by the resonating fan shed new light on the detailed flow phenomena involved, and may help guide future design and optimization of micro scale fans/mixers based on this principle.
On the design of stable state dependent switching laws for single-input single-output systems (2006)

We provide a constructive method for finding stabilising state-dependent switching laws to orchestrate switching between a set of linear vector fields. The method requires that some convex combination of the vector fields should be Hurwitz; no assumptions are made about stability of the individual vector fields.