gebhart/patrepeval huggingface dataset:
A Gene Cluster Encoding Resistomycin Biosynthesis in Streptomyces resistomycificus; Exploring Polyketide Cyclization beyond Linear and Angucyclic Patterns (2004)

Resistomycin is a pentacyclic polyketide metabolite of Streptomyces resistomycificus that exhibits a variety of pharmacologically relevant properties. While virtually all bacterial aromatic polyketides can be grouped into linear and angular polyphenols, resistomycin has a unique "discoid" ring system. We have successfully identified the entire gene cluster encoding resistomycin biosynthesis by heterologously expressing a pooled cosmid library and screening for the fluorescence of the metabolite produced. The rem gene cluster exhibits several unusual features of the type II PKS involved, most remarkably a putative MCAT with highest homology to AT domains from modular PKSs. In addition, we provide the first insight into the molecular basis of a unique mode of cyclization giving rise to a discoid polyketide.
Comparison of Numerically Modeled Knee Joint Contact Forces to Instrumented Total Knee Prosthesis Forces (2009)

Total knee replacement (TKR) surgery decreases pain and increases functional mobility for patients with joint disease. As primary TKRs are implanted in patients who are younger, heavier, and more active (1), increases in wear and TKR revision rates are expected. Preclinical analysis of TKRs with mathematical models and experimental tests require accurate in vivo kinetic and kinematic input data. Kinematics can be obtained with gait analysis, but in vivo force data are just beginning to become available from instrumented TKRs from only a few patients (2). Patient gait is highly variable both within and between individuals and can be influenced by a variety of factors including the progression and history of joint disease, surgical procedure, and TKR design. Variation in patient gait and activities results in subsequent contact force and polyethylene wear variability. A validated mathematical model which calculates contact forces for alternate input data could add valuable insight for preclinical testing. A problem facing mathematical modeling is that there are too many unknowns to directly solve for contact forces. In order to approach this problem, we have developed a knee mathematical model that allows parametric variation of muscle activation levels (3) and calculates a solution space of physically possible contact forces.
Non-Standalone 5G NR FiWi System Based on a Photonic Integrated Multi-Wavelength Transmitter (2021)

This letter presents a non-standalone 5G new radio (NR) multiband fiber-wireless (FiWi) system implemented using an integrated multi-wavelength transmitter with direct modulation. In this system, three 4G/5G RF signals are simultaneously transported over a 12.5-km long radio over fiber (RoF) link, before being amplified and radiated: a 20-MHz 5G NR signal at 788 MHz; five 20-MHz LTE subcarriers at 2.6 GHz; a 100-MHz 5G NR signal at 3.5 GHz. Wireless transmissions through a 10-m long indoor picocell-like link and a 115-m long realistic outdoor wireless link are demonstrated. All 4G and 5G received signals comply with the 3GPP Release 15 requirements, in terms of EVM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RMS</sub> , except for 16 QAM at 3.5 GHz on the 115-m link. Experimental results demonstrate a total throughput of 1.36 Gbit/s and 230 Mbit/s on the 10-m and 115-m scenarios, respectively.
IMMU-32. SPERMIDINE DRIVES GLIOBLASTOMA PROGRESSION VIA SELECTIVE MODULATION OF THE IMMUNE SYSTEM (2022)

Abstract Glioblastoma (GBM) is incurable despite aggressive standard of care treatments (maximal safe surgical resection, radiation, chemotherapy). GBM therapeutic resistance is due to multiple factors, including tumor heterogeneity and a highly immunosuppressive environment. Naturally occurring polyamines have been identified as a putative therapeutic target in other cancers based on their increased presence and function in normal conditions; they are critical for cell growth and proliferation and cellular functions including autophagy and apoptosis. While polyamines are increased in GBM patients, little is known about their impact on GBM growth. In syngeneic immune competent mouse glioma models (GL261, SB28), mass spectrometry data revealed that spermidine (SPD) – a member of the polyamine family – is increased in tumor tissue as compared to non-neoplastic control brain tissue (sham implanted animals). To test the impact of SPD on tumor growth, we treated mouse glioma models with exogenous SPD and found treatment significantly decreased survival. However, in immunocompromised host mice, no such difference was observed, indicating the mechanism through which SPD is driving GBM progression likely involves immune system alterations. Depletion of myeloid derived suppressor cells in vivo via anti-Gr-1 antibody rescues the decrease in survival caused by exogenous SPD, indicating that SPD drives GBM by affecting immune-suppressive cell subsets, namely MDSCs. To assess if SPD is associated with more aggressive GBM growth in human patients, we are currently analyzing polyamine levels in human GBM samples of long vs short term survivors. We are also exploring the effect of dietary polyamines on GBM via the gut-brain-microbiome axis, as polyamines are enriched in many foods and produced by a subset of commensal gut microbes. Understanding the interactions between polyamines, the tumor microenvironment, and the immune response provide a new mechanism for GBM regulation and identify opportunities to alter the environment in the body to enhance immunotherapeutic efficacy.
Retinoic acid induces the differentiation of B cell hybridomas from patients with common variable immunodeficiency. (1988)

Human-human B cell hybridomas constructed from B lymphocytes of common variable immunodeficiency (CVI) patients and the nonsecreting cell line WIL2/729 HF consistently secrete low levels of Ig and appear to retain a defect characteristic of the CVI patient's B cells. We assessed the differentiative capacity of retinoic acid (RA) on these hybridomas, as well as on hybridomas constructed from normal B cells and from patients with selective IgA deficiency. RA at concentrations varying between 10(-5) and 10(-9) M augmented IgM secretion 4-20-fold from four of four CVI hybridomas tested, but did not affect Ig secretion from normal or IgA-deficiency hybridomas. In support of this elevated Ig secretion, RA enhanced the de novo synthesis of biosynthetically labeled light (kappa) and heavy (mu) Ig (up to 4- and 15-fold, respectively) in the CVI hybridoma line JK32.1. The increase in IgM synthesis/secretion could not be accounted for by RA-induced alteration in the cell cycle. In inducing this increase in IgM production, RA was found to affect two aspects of Ig gene expression: (a) the steady-state levels of heavy and light chain mRNAs were enhanced, and (b) the processing of mu heavy chain transcripts to the secreted mRNA form became favored over the membrane mRNA form. We also show that expression of Leu-17 (CD38), a surface marker that is re-expressed in the late pre-plasma stage of B cell development, was increased by RA from less than 20% to greater than 90% of the total cell population, with a concomitant 4-10-fold augmentation in the mean fluorescence intensity. Changes in both Leu-17 expression and de novo Ig synthesis were prominent by 24 h, but could be observed as early as 8 h after induction. Taken together, our study demonstrates that RA affects a marked alteration in the differentiated state of the CVI hybridoma clones. This finding suggests that retinoids can enhance the functional capabilities of B cells with defects in maturation and support further studies to evaluate their clinical potential in CVI.
Uncertainty Quantification for the Extended and the Deterministic-Gain Kalman Filters (2022)

This paper is aimed at characterizing the mean square error and probabilistic uncertainty of a popular class of filtering algorithms in nonlinear systems. The state estimation error of the extended Kalman filter and the deterministic-gain Kalman filter are analyzed. We allow a vector state, but assume scalar measurements. A set of conditions for the mean square error to be upper-bounded is derived. Furthermore, the probabilistic bounds for the estimation error are computed via both the moment-based approach and the stochastic comparison analysis approach. The latter provides a formal means determining uncertainty bounds, such as statistical confidence regions.
Advantages and disadvantages of using various fiber optic sensors in fracture mechanics (1993)

An experimental study is conducted to evaluate the performance of different fiber optic sensors in fracture mechanics applications. A variety of measurement systems, using optical fibers as sensors, were used with simple fracture specimens to determine static and dynamic stress intensity factors and also the location of the crack. The values thus obtained, were compared with theoretical solutions or results obtained from other experimental techniques. The results show the successful application of fiber optic sensors both in attached and embedded configurations, and thus open up the possibility of using them in a host of applications where conventional sensors prove inadequate. Besides describing the various sensors and the results obtained from them, this paper emphasizes the advantages associated with certain configurations of the fiber optic sensors and points out the drawbacks with others.
Comment on ‘The effect of single-particle charge limits on charge distributions in dusty plasmas’ (2016)

It was recently suggested that the electron affinity may pose an additional upper limit on the charge of a single particle in a plasma, in addition to the electron field emission limit. Here we will, however, show that these two limits both rely on the same physical process and that the limit is only relevant for small particles, because it relies on electron tunneling. Plasma-produced particles of only several nanometres (≤10 nm) in size are actively studied, for example in the application of quantum dots and the implications of the proposed charge limit are certainly significant there. However, care must be taken to extend the results to larger particles, which are also actively studied in the field of dusty plasma physics, where typically the limit can be neglected, as we will also show.
Chasing the elusive mammalian microautophagy (2011)

Different mechanisms for delivery of intracellular components (proteins and organelles) to lysosomes and late endosomes for degradation co-exist in almost all cells and set the basis for distinct autophagic pathways. Cargo can be sequestered inside double-membrane vesicles (or autophagosomes) and reach the lysosomal compartment upon fusion of these vesicles to lysosomes through macroautophagy. In a different type of autophagy, known as chaperone-mediated autophagy (CMA), single individual soluble proteins can be targeted one by one to the lysosomal membrane and translocated into the lumen for degradation. Direct sequestration of proteins and organelles by invaginations at the lysosomal membrane that pinch off into the lumen has also been proposed. This process, known as microautophagy, remains poorly understood in mammalian cells. In our recent work, we demonstrate the occurrence of both "in bulk" and "selective" internalization of cytosolic components in late endosomes and identify some of the molecular players of this process that we have named endosomalmicroautophagy (e-MI) due to its resemblance to microautophagy.
Guard time optimisation and adaptation for energy efficient multi-hop TSCH networks (2016)

In the IEEE 802.15.4-2015 standard, Time Slotted Channel Hopping (TSCH) aims to guarantee high-level network reliability by keeping nodes time-synchronised. In order to ensure successful communication between a sender and a receiver, the latter starts listening shortly before the expected time of a MAC layer frame's arrival. The offset between the time a node starts listening and the estimated time of frame arrival is called guard time and it aims to reduce the probability of missed frames due to clock drift. In this paper, we investigate the impact of the guard time on network performance. We identify that, when using the 6tisch minimal schedule, the most significant cause of energy consumption is idle listening during guard time. Therefore, we first perform mathematical modelling on a TSCH link to identify the guard time that maximises the energy-efficiency of the TSCH network in single hop topology. We then continue in multi-hop network, where we empirically adapt the guard time locally at each node depending its distance, in terms of hops, from the sink. Our performance evaluation results, conducted using the Contiki OS, demonstrate that the proposed decentralised guard time adaptation can reduce the energy consumption by up to 40%, without compromising network reliability.
TOWARDS CYCLE-ORIENTED TRACEABILITY IN ENGINEERING CHANGE MANAGEMENT (2014)

Engineering changes and requirement changes strongly interfere with each other. Traceability helps to formalize this interface on a process and organizational level. We propose a data model that includes information elements for different change stages and all related requirement artifacts, solution artifacts or production artifacts. It facilitates the access to necessary information about relations or dependencies between these artifacts. Hence, change effects can easily be estimated and relevant people/information for the decision about a change and its implementation can be identified.
Monitoring Gene Expression To Evaluate Oxygen Infusion at a Gasoline-Contaminated Site (2010)

Increasingly, molecular biological tools, most notably quantitative polymerase chain reaction (qPCR), are being employed to provide a more comprehensive assessment of bioremediation of petroleum hydrocarbons and fuel oxygenates. While qPCR enumeration of key organisms or catabolic genes can aid in site management decisions, evaluation of site activities conducted to stimulate biodegradation would ideally include a direct measure of gene expression to infer activity. In the current study, reverse-transcriptase (RT) qPCR was used to monitor gene expression to evaluate the effectiveness of an oxygen infusion system to promote biodegradation of BTEX and MTBE. During system operation, dissolved oxygen (DO) levels at the infusion points were greater than 30 mg/L, contaminant concentrations decreased, and transcription of two aromatic oxygenase genes and Methylibium petroleiphilum PM1-like 16S rRNA copies increased by as many as 5 orders of magnitude. Moreover, aromatic oxygenase gene transcription and PM1 16s rRNA increased at downgradient locations despite low DO levels even during system operation. Conversely, target gene expression substantially decreased when the system was deactivated. RT-qPCR results also corresponded to increases in benzene and MTBE attenuation rates. Overall, monitoring gene expression complemented traditional groundwater analyses and conclusively demonstrated that the oxygen infusion system promoted BTEX and MTBE biodegradation.
Tonotopic Order in the Adult and Developing Auditory System of the Rat as Shown by c‐fos Immunocytochemistry (1992)

Immediate early genes such as the proto-oncogene c-fos can be expressed in neurons following synaptic excitation by sensory stimulation. C-fos immunocytochemistry has subsequently been shown to be a very sensitive marking technique for neuronal activity. Here, antibodies against the c-fos protein product Fos were used to map the tonotopic organization in the auditory system of adult and developing rats. After stimulating adult rats with pure-tone pulses, bands of Fos-immunoreactive neurons revealed the frequency representation in seven brainstem nuclei: all three subdivisions of the cochlear nucleus, the lateral superior olive, the medial nucleus of the trapezoid body, the ventral nucleus of the trapezoid body, the rostral periolivary nucleus, the dorsal nucleus of the lateral lemniscus and the inferior colliculus. With the exception of the dorsal cochlear nucleus and the inferior colliculus, tonotopicity has not been previously demonstrated in the brainstem nuclei of the rat. During development two striking results were obtained. First, beginning at postnatal day 14 (i.e. approximately 2 days after physiological hearing begins in rats), not only low but also high frequencies were able to induce strong Fos immunoreactivity, indicating that gradual recruitment of formerly unresponsive high-frequency sites does not occur in the rat. Second, a gradual age-related shift of the position of isofrequency bands was not seen in any of the nuclei, suggesting that changes in frequency - place code do not occur after 2 weeks postnatally. These results indicate that the rat's auditory brainstem nuclei achieve their adult-like tonotopic organization early on, implying a somewhat different developmental time course than is found in other mammalian species.
Location of conjugated diene position in an aliphatic chain by mass spectrometry of the 4-phenyl-1,2,4-triazoline-3,5-dione adduct (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLocation of conjugated diene position in an aliphatic chain by mass spectrometry of the 4-phenyl-1,2,4-triazoline-3,5-dione adductDavid C. Young, Paul. Vouros, Brian. Decosta, and Michael F. HolickCite this: Anal. Chem. 1987, 59, 15, 1954–1957Publication Date (Print):August 1, 1987Publication History Published online1 May 2002Published inissue 1 August 1987https://pubs.acs.org/doi/10.1021/ac00142a013https://doi.org/10.1021/ac00142a013research-articleACS PublicationsRequest reuse permissionsArticle Views253Altmetric-Citations29LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Abstract 19466: Testosterone Levels and Risk for Cardiovascular Events - A Report From the ORIGIN (Outcome Reduction With an Initial Glargine Intervention) Trial (2017)

Introduction: Low testosterone levels have been associated with increased risk for cardiovascular diseases and glucose perturbations in population-based studies. Information on the prognostic abili...
Macrolide Treatment Inhibits Pseudomonas aeruginosa Quorum Sensing in Non–Cystic Fibrosis Bronchiectasis. An Analysis from the Bronchiectasis and Low-Dose Erythromycin Study Trial (2016)

We demonstrate inhibition of P. aeruginosa quorum sensing within the airways of patients with non-cystic fibrosis bronchiectasis receiving long-term, low-dose erythromycin, without a reduction in bacterial load, representing a potential mechanism of therapeutic impact beyond a classical antimicrobial or antiinflammatory pathway.
A C-Terminal Fragment of Chlorotoxin Retains Bioactivity and Inhibits Cell Migration (2019)

Chlorotoxin was originally isolated from the venom of the Israeli scorpion <i>Leiurus quinquestriatus</i>, and has potential as a tumor imaging agent based on its selective binding to tumor cells. Several targets have been suggested for chlorotoxin including voltage-gated chloride channels, and it has been shown to have anti-angiogenic activity and inhibit cell migration. The structure of chlorotoxin is stabilized by four disulfide bonds and contains β-sheet and helical structure. Interestingly, the reduced form has previously been shown to inhibit cell migration to the same extent as the wild type, but structural analysis indicates that the reduced form of the peptide does not maintain the native secondary structure and appears unstructured in solution. This lack of structure suggests that a short stretch of amino acids might be responsible for the bioactivity. To explore this hypothesis, we have synthesized fragments of chlorotoxin without disulfide bonds. As expected for such small peptides, NMR analysis indicated that the peptides were unstructured in solution. However, the peptide corresponding to the eight C-terminal residues inhibited cell migration, in contrast to the other fragments. Our results suggest that the C-terminal region plays a critical role in the bioactivity of chlorotoxin.
Does the direct lateral approach to the hip joint jeopardize the superior gluteal nerve? (1991)

Abstract The purpose of this anatomical study was to determine the location and course of the superior gluteal nerve in relation to the superior pole of the greater trochanter and the surgical pathway for the direct lateral approach to the hip joint. Twenty adult cadaveric lower extremities in ten patients (five male and five female) were carefully dissected to identify the location of the superior gluteal nerve and its terminal branches. The most inferior branch of the superior gluteal nerve was variable, could be asymmetrical, and was located 3–6.5 cm above the superior tip of the greater trochanter. During the lateral approach to the hip, it is recommended that the proximal extension be limited to 3 cm above the most superior aspect of the greater trochanter.
Improved hands-free automatic speech recognition in reverberant environment condition (2014)

In this paper, we incorporate language information in the treatment of reverberation in a microphone array system. First, microphone array processing is used to spatially filter the observed multiple sources. Second, the separated signal is enhanced to remove the effects of reverberation. Then, we extract information concerning the impact of smearing to the language (word sequence) used in the automatic speech recognition (ASR) system. Consequently, we compute the language-inferred coefficients via offline training. During online testing, the language-inferred coefficients are employed in conjunction with an enhancement scheme. The coefficients reflect the realistic impact of smearing in conjunction with the language information. As a result, the enhanced signal is more effective in ASR application. Experimental results in a real environment condition show that the proposed method outperforms the conventional methods that exclude language information. Moreover, we show the recognition results comparing the proposed method against existing dereverberation methods.
Evaluation of spoken language grammar learning in the ATIS domain (2002)

To facilitate the development of speech enabled applications and services, researchers have been working on a variety of smart tools. Recently we have introduced a schema-based context free grammar learning algorithm aiming at the development of real applications. In that paper we have described the algorithm and given some experimental results on the data of our in-house project. To study the general applicability of the algorithm as well as to provide the research community with more informative results, we have applied the algorithm to the well studied ATIS task and compared the performance of the learned grammar with one of the best performers in ATIS evaluations. The results show that the semi-automatically learned grammar achieves comparable performance to the manually authored grammar.