gebhart/patrepeval huggingface dataset:
The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation (2016)

Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin) with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD) to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325). Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, R. gnavus, Flavonifractor plautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal trophic chain with the potential to highly impact the metabolic balance as well as the gut microbiota/host homeostasis by the formation of different short chain fatty acids.
Synthesis of catalytic materials in flames: opportunities and challenges (2016)

The proven capacity of flame aerosol technology for rapid and scalable synthesis of functional nanoparticles makes it ideal for the manufacture of an array of heterogeneous catalysts. Capitalizing on the high temperature environment, rapid cooling and intimate component mixing at either atomic or nano scale, novel catalysts with unique physicochemical properties have been made using flame processes. This tutorial review covers the main features of flame synthesis and illustrates how the physical and chemical properties of as-synthesized solid catalytic materials can be controlled by proper choice of the process parameters. Gas phase particle formation mechanisms and the effect of synthesis conditions (reactor configuration, precursor and dispersion gas flow rates, temperature and concentration fields) on the structural, chemical and catalytic properties of as-prepared materials are discussed. Finally, opportunities and challenges offered by flame synthesis of catalytic materials are addressed.
Estimation of Markov Chain Transition Probabilities and Rates from Fully and Partially Observed Data: Uncertainty Propagation, Evidence Synthesis, and Model Calibration (2005)

Markov transition models are frequently used to model disease progression. The authors show how the solution to Kolmogorov's forward equations can be exploited to map between transition rates and probabilities from probability data in multistate models. They provide a uniform, Bayesian treatment of estimation and propagation of uncertainty of transition rates and probabilities when 1) observations are available on all transitions and exact time at risk in each state (fully observed data) and 2) observations are on initial state and final state after a fixed interval of time but not on the sequence of transitions (partially observed data). The authors show how underlying transition rates can be recovered from partially observed data using Markov chain Monte Carlo methods in WinBUGS, and they suggest diagnostics to investigate inconsistencies between evidence from different starting states. An illustrative example for a 3-state model is given, which shows how the methods extend to more complex Markov models using the software WBDiff to compute solutions. Finally, the authors illustrate how to statistically combine data from multiple sources, including partially observed data at several follow-up times and also how to calibrate a Markov model to be consistent with data from one specific study.
A statistical study on shale properties: Relationships among principal shale properties (2020)

Our study has been carried out to develop models for predicting mechanical behaviour of shales using available geological information and index properties. A statistical analysis has been performed; relationships among some index properties, geological data, and mechanical properties are presented. Such relationships may be of use for petroleum engineers in stability analysis during drilling and production, and for civil engineers in foundations, dams, and underground excavations, thus these models may aid preliminary estimates of properties and perhaps even reduce testing requirements.
The future generation of software: a management perspective (1991)

The engineering process that underlies software development is examined. A brief summary of how information technology has affected both institutions and individuals in the past few decades is given. Engineering with models and metrics is then discussed. Improving software quality, making software engineering technology more transferable, and transferring software technology into an organization are addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
FDA Approval Summary: Mylotarg for Treatment of Patients with Relapsed or Refractory CD33-Positive Acute Myeloid Leukemia (2018)

Gemtuzumab ozogamicin (GO) 3 mg/m<sup>2</sup> days 1, 4, and 7 is an active regimen for induction of remission when used to treat patients with relapsed or refractory CD33-positive acute myeloid leukemia without curative intent. The risks of hepatic veno-occlusive disease and early mortality with this regimen appear to be lower than reported previously for GO 9 mg/m<sup>2</sup> days 1 and 15. The data were not sufficient to enable conclusions about the safety of GO in children younger than 2 years of age.
Gabapentin Monotherapy for the Symptomatic Treatment of Painful Neuropathy: A Multicenter, Double‐blind, Placebo‐controlled Trial in Patients With Diabetes Mellitus<sup>1</sup> (1999)

Pain is the most disturbing symptom of diabetic neuropathy. Traditionally this type of pain was treated with tricyclic antidepressants which frequently have many side effects. In the study reported here, gabapentin was administered in escalating doses up to 3600 mg per day to eligible patients with moderate to severe diabetic neuropathy pain in a double blind placebo controlled fashion. Gabapentin provided superior and significant pain relief over placebo. In addition, patients taking gabapentin had improvement of sleep scores and a number of items on mood and quality of life questionnaires. Gabapentin was tolerated well with mild and tolerable side effects.
A multi-mode excitation hardness prediction method based on controlled laser air-force detection (CLAFD) technique (2019)

A novel material hardness testing method was proposed based on controlled laser air-force detection (CLAFD) technique. Polyurethane was chosen as the study object. Multi-mode excitation was adopted. Partial least square as the modeling method was used to build the hardness prediction model on the data of laser displacement. Different preprocessing methods were carried out for eliminating the noise of the original data. The results showed the multiplicative scattering correction (MSC) had the best performance. Among four modes, the relationship coefficients of the prediction set (Rp) was above 0.90, and the residual prediction deviation (RPD) was more than 2. This result demonstrated that all four modes could be carried out to test the hardness of polyurethane. Furthermore, the Rp of the transient was 0.93, the RPD was 2.51, the excitation time was 1 s, showing that the transient mode performed with precision in high-speed hardness detection. The highest precision was based on the stress relaxation mode, so we did further study on the interval modeling analysis for the data of stress relaxation mode. The results showed that the hardness could not be predicted if only one single interval was used. However, the performance improved with the increase in the number of intervals. The Rp was up to 0.96, the coefficient of calibration set (Rc) was up to 0.99, and the RPD was 3.54 when the time of the stress relaxation mode lasted 60 s. Based on the results above, the prediction ability would improve further when the relaxation time is increased. The study will provide a new real-time, non-destruction and cross-contamination free hardness detection method for material science, especially for those materials such as artificial biological tissue, function food products, etc.
Identification of the Herboxidiene Biosynthetic Gene Cluster in Streptomyces chromofuscus ATCC 49982 (2012)

The 53-kb biosynthetic gene cluster for the novel anticholesterol natural product herboxidiene was identified in Streptomyces chromofuscus ATCC 49982 by genome sequencing and gene inactivation. In addition to herboxidiene, a biosynthetic intermediate, 18-deoxy-herboxidiene, was also isolated from the fermentation broth of S. chromofuscus ATCC 49982 as a minor metabolite.
Potent anti-feline immunodeficiency virus and anti-human immunodeficiency virus effect of IFN-tau (1997)

Ovine IFN-tau is a newly described protein related to IFN-alpha that is responsible for maternal recognition of pregnancy in sheep. It has been shown to exhibit potent antiviral and antiproliferative activity. To determine its antiviral activity against feline immunodeficiency virus (FIV) and HIV, the activity of the RNA-dependent DNA polymerase, reverse transcriptase, was assayed in FIV- and HIV-infected feline and human PBL treated with IFN-tau. Significant dose-dependent inhibition of reverse transcriptase activity by IFN-tau was detected by day 6 of culture and was maintained through the peak of virus replication. In addition, production of the FIV core protein, p25, was blocked by IFN-tau. Both the amino- and carboxyl-terminal regions of IFN-tau, as identified by synthetic peptides, appear to be involved in its antiretroviral activity. Comparison of the anti-HIV activities of IFN-tau and recombinant human IFN-alpha2 (rHuIFN-alpha2) indicated that while rHuIFN-alpha2 was toxic to cells at 10,000 U/ml, IFN-tau antiretroviral activity was not associated with a decrease in either cell viability or immunologic reactivity. Thus, IFN-tau displayed potent anti-FIV and anti-HIV activity without the cytotoxicity associated with high concentrations of rHuIFN-alpha2.
Design of low power ASK CMOS demodulator circuit for RFID tag: Design of All-MOSFET low power ASK demodulator (2010)

In this paper, Amplitude Shift Keying (ASK) demodulator of Radio Frequency Identification (RFID) tag module is designed as low power. RFID tag is pursued the least area, low price and low power. And the proposed ASK demodulator is designed without resistors and capacitors, differing from the existing ASK demodulator. Also, the proposed ASK demodulator is designed without envelope detector and Schmitt-trigger at a minimum of mosfet. In this paper, we presented a circuit of two ASK demodulator. We tested designed ASK demodulator using HSPICE. The design has been verified and realized by using a TSMC (Taiwan Semiconductor Manufacturing Company), and used 900MHz of amplitude modulation signal as input signal. As a result, average power consumption spent 7.065uW, and maximum power consumption spent 41uW.
Genomic Copy Number Determines Functional Expression of β-Defensin 2 in Airway Epithelial Cells and Associates with Chronic Obstructive Pulmonary Disease (2010)

Genomic copy number variation of beta-defensin encoding genes has a functional role in airway epithelial cells, which may contribute to the pathogenesis of COPD.
Effects of adipose stem cell-conditioned medium on the migration of vascular endothelial cells, fibroblasts and keratinocytes (2016)

[This retracts the article DOI: 10.3892/etm.2013.887.].
Block-level Virtualization: How far can we go? (2006)

In this paper, we present our vision on building large-scale storage systems from commodity components in a data center. For reasons of efficiency and flexibility, we advocate maintaining sophisticated data management functions behind a block-based interface. We anticipate that such an interface can be customized to meet the diverse needs of end-users and applications through the extensible storage system architecture that we propose.
Peripheral nerve‐stimulated macrophages simulate a peripheral nerve‐like regenerative response in rat transected optic nerve (1998)

We have previously demonstrated that the failure of the mammalian central nervous system (CNS) to regenerate following axonal injury is related to its immunosuppressive nature, which restricts the ability of both recruited blood-borne monocytes and CNS-resident microglia to support a process of repair. In this study we show that transected optic nerve transplanted with macrophages stimulated by spontaneously regenerating nerve tissue, e.g., segments of peripheral nerve (sciatic nerve), exhibit axonal regrowth at least as far as the optic chiasma. Axonal regrowth was confirmed by double retrograde labeling of the injured optic axons, visualized in their cell bodies. Transplanted macrophages exposed to segments of CNS (optic) nerve were significantly less effective in inducing regrowth. Immunocytochemical analysis showed that the induced regrowth was correlated with a wide distribution of macrophages within the transplanted-transected nerves. It was also correlated with an enhanced clearance of myelin, known to be inhibitory for regrowth and poorly eliminated after injury in the CNS. These results suggest that healing of the injured mammalian CNS, like healing of any other injured tissue, requires the partnership of the immune system, which is normally restricted, but that the restriction can be circumvented by transplantation of peripheral nerve-stimulated macrophages.
SIPS, A Structural Integrity Prognosis System (2007)

The Structural Integrity Prognosis System (SIPS) is being designed to provide prompt, informed predictions of the structural viability of individual assets based on tracking of their actual use and modeling of anticipated usage. The prognosis system is founded on a collaboration between sensor systems, advanced reasoning methods for data fusion and signal interpretation, and modeling and simulation systems. The modeling approach is based on the physical mechanisms of corrosion and fatigue damage. This paper will present an overview of the system and present recent results of laboratory testing of fatigue coupons that were representative of a typical aircraft lower wing structure. During the tests, several novel sensor systems were used to detect and quantify fatigue damage. The sensor output was combined with results from several models of fatigue damage. The models were based on the microstructural origins of fatigue, and included statistical distributions of important microstructural parameters. The models and the sensor data were combined in a prognosis system, and used to predict the outcome of the fatigue tests.. Uncertainty in the sensor data and uncertainty in the various models and their microstructural inputs was explicitly dealt with in the prognosis system. The predictions were compared to post-mortem analysis of cracking in the broken samples.
<title>Arrayed waveguide grating demultiplexers in silicon-on-insulator</title> (2000)

This paper presents theoretical and experimental results detailing the design and performance of arrayed waveguide grating (AWG) demultiplexers fabricated in silicon-on- insulator (SOI). The SOI waveguide is inherently multimode because of the high refractive index difference between Si and SiO<SUB>2</SUB>, although appropriate tailoring of the rib width to height ratio can be used to make single mode rib waveguides. This single mode condition cannot be met in the input and output combiner sections, which can therefore support many higher order modes. Modeling results demonstrate that coupling from a single mode ridge waveguide to the fundamental slab mode is typically two orders of magnitude larger than the coupling to higher modes. Hence the effect of multimode combiners on performance should be minimal. We also present calculations of bending losses which indicate that with a Si thickness of 1.5 micrometers , single mode rib waveguides can be made with radii of curvature as low as 200 micrometers . Such waveguides can also be made with zero birefringence. AWG devices were fabricated with 8 channels centered around (lambda) equals 1550 nm, and chip sizes less than 5 X 5 mm. The performance of these devices is compared with our modeling results.
Measurement system of optical properties of vertebra bones on near-infrared spectrum (2013)

Near-infrared spectrum scattered from biological tissue can be used to characterize the optical properties of the tissues. If the optical properties of different parts of vertebra bones are different, a new navigation method in pedicle screw insertion surgery can be proposed. The goal of this study is to develop an optical measurement method which can detect the optical properties of vertebra bones on near-infrared spectrum. A 2.0-mmdiameter steel probe containing two 200-micron diameter optic fibers was used to deliver light and collect light spectrum from the surface of vertebra bones. In experiment, the integrated pig vertebra bones were split. The steel probe was put on the different position of the anatomical section and the spectrum was detected at each point. The optical properties deduced from the spectrum were distinguished between the cortical bones and cancellous bones in the trajectory of pedicle screw placement.
Stability and Stabilizability of Switched Linear Systems: A Survey of Recent Results (2009)

During the past several years, there have been increasing research activities in the field of stability analysis and switching stabilization for switched systems. This paper aims to briefly survey recent results in this field. First, the stability analysis for switched systems is reviewed. We focus on the stability analysis for switched linear systems under arbitrary switching, and we highlight necessary and sufficient conditions for asymptotic stability. After a brief review of the stability analysis under restricted switching and the multiple Lyapunov function theory, the switching stabilization problem is studied, and a variety of switching stabilization methods found in the literature are outlined. Then the switching stabilizability problem is investigated, that is under what condition it is possible to stabilize a switched system by properly designing switching control laws. Note that the switching stabilizability problem has been one of the most elusive problems in the switched systems literature. A necessary and sufficient condition for asymptotic stabilizability of switched linear systems is described here.
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research (2020)

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the "ARRIVE Essential 10," which constitutes the minimum requirement, and the "Recommended Set," which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration (E&E) document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
FIMM, a database of functional molecular immunology (2000)

FIMM database (http://sdmc.krdl.org.sg:8080/fimm ) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a set of search tools for extraction of information and results are presented as lists or as reports.
A proteomic approach identifies early pregnancy biomarkers for preeclampsia: Novel linkages between a predisposition to preeclampsia and cardiovascular disease (2009)

Preeclampsia (PE) is a common, potentially life-threatening pregnancy syndrome triggered by placental factors released into the maternal circulation, resulting in maternal vascular dysfunction along with activated inflammation and coagulation. Currently there is no screening test for PE. We sought to identify differentially expressed plasma proteins in women who subsequently develop PE that may perform as predictive biomarkers. In seven DIGE experiments, we compared the plasma proteome at 20 wk gestation in women who later developed PE with an appropriate birth weight for gestational age baby (n=27) or a small for gestational age baby (n=12) to healthy controls with uncomplicated pregnancies (n=57). Of the 49 differentially expressed spots associated with PE-appropriate for gestational age, PE-small for gestational age or both (p<0.05, false discovery rate corrected), 39 were identified by LC-MS/MS. Two protein clusters that accurately (>90%) classified women at risk of developing PE were identified. Immunoblots confirmed the overexpression of fibrinogen gamma chain and alpha-1-antichymotrypsin in plasma prior to PE. The proteins identified are involved in lipid metabolism, coagulation, complement regulation, extracellular matrix remodeling, protease inhibitor activity and acute-phase responses, indicating novel synergism between pathways involved in the pathogenesis of PE. Our findings are remarkably similar to recently identified proteins complexed to high-density lipoprotein and linked to cardiovascular disease.