gebhart/patrepeval huggingface dataset:
Enhanced Glucose Consumption and Organic Acid Production by Engineered Corynebacterium glutamicum Based on Analysis of a pfkB1 Deletion Mutant (2016)

In the analysis of a carbohydrate metabolite pathway, we found interesting phenotypes in a mutant strain of Corynebacterium glutamicum deficient in pfkB1, which encodes fructose-1-phosphate kinase. After being aerobically cultivated with fructose as a carbon source, this mutant consumed glucose and produced organic acid, predominantly l-lactate, at a level more than 2-fold higher than that of the wild-type grown with glucose under conditions of oxygen deprivation. This considerably higher fermentation capacity was unique for the combination of pfkB1 deletion and cultivation with fructose. In the metabolome and transcriptome analyses of this strain, marked intracellular accumulation of fructose-1-phosphate and significant upregulation of several genes related to the phosphoenolpyruvate:carbohydrate phosphotransferase system, glycolysis, and organic acid synthesis were identified. We then examined strains overexpressing several of the identified genes and demonstrated enhanced glucose consumption and organic acid production by these engineered strains, whose values were found to be comparable to those of the model pfkB1 deletion mutant grown with fructose. l-Lactate production by the ppc deletion mutant of the engineered strain was 2,390 mM (i.e., 215 g/liter) after 48 h under oxygen deprivation, which was a 2.7-fold increase over that of the wild-type strain with a deletion of ppc IMPORTANCE: Enhancement of glycolytic flux is important for improving microbiological production of chemicals, but overexpression of glycolytic enzymes has often resulted in little positive effect. That is presumably because the central carbon metabolism is under the complex and strict regulation not only transcriptionally but also posttranscriptionally, for example, by the ATP/ADP ratio. In contrast, we studied a mutant strain of Corynebacterium glutamicum that showed markedly enhanced glucose consumption and organic acid production and, based on the findings, identified several genes whose overexpression was effective in enhancing glycolytic flux under conditions of oxygen deprivation. These results will further understanding of the regulatory mechanisms of glycolytic flux and can be widely applied to the improvement of the microbial production of useful chemicals.
Why do vertical steps reappear in adsorption isotherms? (1993)

On the basis of an extensive set of vapor pressure isotherm and diffraction measurements and computer simulations, we present a microscopic description of the mechanism responsible for the observations of Youn and Hess, Phys. Rev. Lett. 64, 918 (1990), relating to the (reentrant) layering properties of argon-on-graphite films. In the neighborhood of 67 K (and for films more than one layer thick) a transition region exists where the outermost solid layer becomes liquid by a coverage driven process involving layer promotion. Once formed, the liquid layer can be ``re'' solidified by further increases in argon coverage. This advancing solid-liquid interface results in (re)appearance of vertical steps in the isotherms.
The Protective Effect of Adenocaulon himalaicum Edgew. and Its Bioactive Compound Neochlorogenic Acid against UVB-Induced Skin Damage in Human Dermal Fibroblasts and Epidermal Keratinocytes (2021)

Skin aging induced by ultraviolet (UV) irradiation increases expression of matrix metalloproteinase-1 (MMP-1) and destroys collagen fibers, as a result accelerating wrinkle formation. Natural products have been received scientific attention as utilized agents against photoaging. The aim of this study was to investigate the protective effect of <i>Adenocaulon himalaicum</i> Edgew. extract (AHE) against ultraviolet B (UVB)-induced skin damage, and to explain the underlying mechanisms in human dermal fibroblasts and epidermal keratinocytes. AHE effectively protects skin photoaging by preventing collagen degradation through MMP-1 inhibition via the MAPK/AP-1 signaling pathway. AHE significantly increased the expression of skin hydration factors, such as filaggrin, involucrin, loricrin, and caspase-14. To find how AHE possesses a direct impact on cellular activities, we identified neochlorogenic acid as a bioactive component of AHE for the first time. Neochlorogenic acid showed the anti-photoaging effect through ameliorating UVB-induced collagen degradation, reinforcing the skin barrier. Like the AHE-regulating mechanism, neochlorogenic acid modulates the MAPK/AP-1 signaling pathway and skin hydration factors. Taken together, these results suggest that AHE and neochlorogenic acid are well-qualified candidate for enhancing the conditions of photoaged skin.
Characteristics of Neuropeptide-Containing Innervation, Tissue Remodeling, Growth, and Vascularity in Noses of Patients With Cleft Lip and Palate (2020)

The moderate expression of TGFβ1 and increased distribution of VEGF, MMP2, MMP9, and TIMP2 demonstrate an active extracellular matrix remodeling and angiogenesis, performed by proteases. The cartilaginous septum of the nose is an example of balance between tissue degradation and its suppression, demonstrated by the relationship between MMPs and TIMPs and the presence of VEGF.
The accuracy of four commercial broth microdilution tests in the determination of the minimum inhibitory concentration of colistin (2020)

Colistin is considered as one of the last-resort antibiotics and reliable antimicrobial susceptibility testing is therefore crucial. The reference standard for AST according to EUCAST and CLSI is broth microdilution (BMD). However, BMD is labor intensive to perform. Commercial antimicrobial susceptibility tests derived from BMD method are available. We investigated the performance of four different commercial tests: Sensititre™, SensiTest™ Colistin, Micronaut MIC Strip Colistin and UMIC Colistin using 70 clinical isolates (half of them was deemed by VITEK2 as resistant), including isolates from cystic fibrosis patients and mcr-1 bearing isolates. We used two reference standards: BMD and composite MIC as determined by all four tests. Sensititre™ had essential agreement (EA, defined as minimum inhibitory concentration within ± 1 dilution) of 87% and 89% compared to BMD and composite reference standard, respectively. For SensiTest™, the EA's were 93% and 90%. For UMIC, 87% and 90%, and for Micronaut, 83% and 84%. All four tests demonstrated categorical agreement (CA) above 90%. CA for SensiTest™ and Micronaut was both 96%, UMIC 94%, and Sensititre™ 93%. All tests were reproducible as tested in two quality control isolates. In conclusion, in clinical isolates from a large referral center, the four commercial tests for determination of colistin minimum inhibitory concentrations showed acceptable performance.
A Consensus on the Diagnosis and Treatment of Acromegaly Comorbidities: An Update (2019)

Evidence-based approach consensus recommendations address important clinical issues regarding multidisciplinary management of acromegaly-related cardiovascular, endocrine, metabolic, and oncologic comorbidities, sleep apnea, and bone and joint disorders and their sequelae, as well as their effects on quality of life and mortality.
Distilling Optimal Neural Networks: Rapid Search in Diverse Spaces (2020)

Current state-of-the-art Neural Architecture Search (NAS) methods neither efficiently scale to multiple hardware platforms, nor handle diverse architectural search-spaces. To remedy this, we present DONNA (Distilling Optimal Neural Network Architectures), a novel pipeline for rapid, scalable and diverse NAS, that scales to many user scenarios. DONNA consists of three phases. First, an accuracy predictor is built using blockwise knowledge distillation from a reference model. This predictor enables searching across diverse networks with varying macro-architectural parameters such as layer types and attention mechanisms, as well as across micro-architectural parameters such as block repeats and expansion rates. Second, a rapid evolutionary search finds a set of pareto-optimal architectures for any scenario using the accuracy predictor and on-device measurements. Third, optimal models are quickly finetuned to training-from-scratch accuracy. DONNA is up to 100x faster than MNasNet in finding state-of-the-art architectures on-device. Classifying ImageNet, DONNA architectures are 20% faster than EfficientNet-B0 and MobileNetV2 on a Nvidia V100 GPU and 10% faster with 0.5% higher accuracy than MobileNetV2-1.4x on a Samsung S20 smartphone. In addition to NAS, DONNA is used for search-space extension and exploration, as well as hardware-aware model compression.
Crystallography (2018)

This chapter considers small-molecule crystallography for the study of molecular and crystal structure. It reviews a brief history of crystallography, and then describes the basic elements of crystal structure, the principles of X-ray diffraction, and the process of determining a crystal structure from diffraction data. Single-crystal X-ray diffraction is unequivocally the most definitive technique for determining crystal structures. All too often, however, the structures of small-molecule crystal forms are elusive because of the single-crystal size/quality requirements of the X-ray methods or the methods of preparation. The chapter also highlights complementary approaches to single-crystal diffraction, namely, structure determination from powder diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy (NMR crystallography), and emerging crystal structure prediction (CSP) methodology. Miller indices are one of the most important concepts in modern crystallography and the chapter further discusses this in detail.
Joint Analysis of Marine Active and Passive Source EM Data for Sub-Salt or Sub-Basalt Imaging (2003)

F-18 JOINT ANALYSIS OF MARINE ACTIVE AND PASSIVE SOURCE EM DATA FOR SUB-SALT OR SUB-BASALT IMAGING Abstract 1 EAGE 65th Conference &amp; Exhibition — Stavanger Norway 2 - 5 June 2003 L.M.MACGREGOR OHM Ltd. Southampton Oceanography Centre U.K. Marine electromagnetic (EM) exploration methods which allow the electrical resistivity of the seafloor to be determined remotely have been developed in the academic sector over the last twenty years and are now being applied widely within the hydrocarbon industry. One area where such techniques can make a significant contribution is in regions where sediments of interest are obscured by (for example) salt
Structure-Function Relationships With Spectral-Domain Optical Coherence Tomography Retinal Nerve Fiber Layer and Optic Nerve Head Measurements (2014)

The structure-function relationship was significantly stronger with BMO-MRW than other ONH SD-OCT parameters. The best diagnostic capabilities were seen with rim area and average RNFL.
Protective effects of immunoactive peptide, FK565 against systemic and local infections with herpes simplex virus and murine cytomegalovirus and respiratory tract infection with influenza virus in mice. (1992)

The protective effects of FK565 against systemic infections with herpes simplex virus (HSV) and murine cytomegalovirus (MCMV), respiratory tract infection with influenza virus and zosteriform rash with HSV investigated in mice. FK565 showed excellent protective activities against systemic infections with both acyclovir (ACV)-sensitive and -resistant HSV at intravenous and subcutaneous doses of 0.1 and 1 mg/kg and oral dose of 1 mg/kg. FK565 showed superior protective activities at subcutaneous doses of 0.01 and 0.1 mg/kg compared to ACV at subcutaneous dose of 15 mg/kg against MCMV infection. In respiratory tract infection with influenza virus, FK565 showed potent protective effects at intravenous, subcutaneous and oral doses of 0.001 to 1 mg/kg. FK565 markedly inhibited zosteriform spread of HSV on the flank skin at an intravenous dose of 0.1 mg/kg and the mice given FK565 survived longer than the control mice. The peritoneal exudate cells from FK565-treated mice suppressed the growth of HSV in mouse embryo fibroblast more strongly than those from the control mice, although FK565 had no direct antiviral activity against HSV. These findings suggest that FK565 enhanced the host defense ability against viral infections by nonspecific activation of macrophages.
Importance of Phase Change of Aluminum in Oxidation of Aluminum Nanoparticles (2004)

Aluminum nanoparticles have increasingly gained attention because of their potential incorporation in explosive and propellant mixtures. This letter reports on a qualitative study on the oxidation of aluminum nanoparticles containing a passivating oxide coating. Hot-stage transmission electron microscopy (TEM) studies were performed to understand the stability of the oxide coating in nanoaluminum, and oxidation was investigated using a single particle mass spectrometer (SPMS). We find that the oxidation of oxide-coated nanoaluminum coincides with and therefore is presumably initiated by melting of the aluminum core and subsequent mechanical rupture of the oxide coating.
The Calm Mouse: An Animal Model of Stress Reduction (2012)

Chronic stress is associated with negative health outcomes and is linked with neuroendocrine changes, deleterious effects on innate and adaptive immunity, and central nervous system neuropathology. Although stress management is commonly advocated clinically, there is insufficient mechanistic understanding of how decreasing stress affects disease pathogenesis. Therefore, we have developed a "calm mouse model" with caging enhancements designed to reduce murine stress. Male BALB/c mice were divided into four groups: control (Cntl), standard caging; calm (Calm), large caging to reduce animal density, a cardboard nest box for shelter, paper nesting material to promote innate nesting behavior, and a polycarbonate tube to mimic tunneling; control exercise (Cntl Ex), standard caging with a running wheel, known to reduce stress; and calm exercise (Calm Ex), calm caging with a running wheel. Calm, Cntl Ex and Calm Ex animals exhibited significantly less corticosterone production than Cntl animals. We also observed changes in spleen mass, and in vitro splenocyte studies demonstrated that Calm Ex animals had innate and adaptive immune responses that were more sensitive to acute handling stress than those in Cntl. Calm animals gained greater body mass than Cntl, although they had similar food intake, and we also observed changes in body composition, using magnetic resonance imaging. Together, our results suggest that the Calm mouse model represents a promising approach to studying the biological effects of stress reduction in the context of health and in conjunction with existing disease models.
One-step preparation of xanthones via Pd-catalyzed annulation of 1,2-dibromoarenes and salicylaldehydes (2009)

A one-step preparation of xanthones via Pd-catalyzed annulation of 1,2-dibromoarenes and salicylaldehydes was developed.
DNMT1 Inhibition Reprograms Pancreatic Cancer Stem Cells via Upregulation of the miR-17-92 Cluster (2016)

Pancreatic ductal adenocarcinoma (PDAC) and other carcinomas are hierarchically organized, with cancer stem cells (CSC) residing at the top of the hierarchy, where they drive tumor progression, metastasis, and chemoresistance. As CSC and non-CSC share an identical genetic background, we hypothesize that differences in epigenetics account for the striking functional differences between these two cell populations. Epigenetic mechanisms, such as DNA methylation, play an important role in maintaining pluripotency and regulating the differentiation of stem cells, but the role of DNA methylation in pancreatic CSC is obscure. In this study, we investigated the genome-wide DNA methylation profile of PDAC CSC, and we determined the importance of DNA methyltransferases for CSC maintenance and tumorigenicity. Using high-throughput methylation analysis, we discovered that sorted CSCs have a higher level of DNA methylation, regardless of the heterogeneity or polyclonality of the CSC populations present in the tumors analyzed. Mechanistically, CSC expressed higher DNMT1 levels than non-CSC. Pharmacologic or genetic targeting of DNMT1 in CSCs reduced their self-renewal and in vivo tumorigenic potential, defining DNMT1 as a candidate CSC therapeutic target. The inhibitory effect we observed was mediated in part through epigenetic reactivation of previously silenced miRNAs, in particular the miR-17-92 cluster. Together, our findings indicate that DNA methylation plays an important role in CSC biology and also provide a rationale to develop epigenetic modulators to target CSC plasticity and improve the poor outcome of PDAC patients. Cancer Res; 76(15); 4546-58. ©2016 AACR.
Laser vacuum acceleration of a relativistic electron bunch (2015)

With regard to the problem of laser acceleration of a relativistic electron bunch we present a scheme of its vacuum acceleration directly by a relativistic intensity laser pulse. The energy of the electron bunch injected into the laser pulse leading edge increases during its coaxial movement to a thin, pulse-reflecting target. The laser-accelerated electrons continue to move free forward, passing through the target. The study of this acceleration scheme in the three-dimensional geometry is verified in a numerical simulation by the particle-in-cell method, which showed that the energy of a part of the electrons can increase significantly compared to the initial one. Restrictions are discussed, which impose limiting values of energy and total charge of accelerated electrons.
An overview of the ESTEC-AKUBA programme (1993)

A study over three years for the design and manufacture of an imaging phased array antenna to provide European multiple spot beam coverage has included extensive trade-off activities, and resulted in the choice of a dual shaped imaging system for breadboarding. This paper presents an overview of the ESTEC active Ku band antenna programme. The design and performance of the antenna are presented. The results of the trade-off study are also summarised.
Semi-automatic video semantic annotation based on active learning (2005)

In this paper, we propose a novel semi-automatic annotation scheme for home videos based on active learning. It is well-known that there is a large gap between semantics and low-level features. To narrow down this gap, relevance feedback has been introduced in a number of literatures. Furthermore, to accelerate the convergence to the optimal result, several active learning schemes, in which the most informative samples are chosen to be annotated, have been proposed in literature instead of randomly selecting samples. In this paper, a representative active learning method is proposed, which local consistency of video content is effectively taken into consideration. The main idea is to exploit the global and local statistical characteristics of videos, and the temporal relationship between shots. The global model is trained on a smaller pre-labeled video dataset, and the local information is obtained online in the process of active learning, and will be used to adjust the initial global model adaptively. The experiment results show that the proposed active learning scheme has significantly improved the annotation performance compared with random selecting and common active learning method.
Dynamic Route Guidance - Status and Trends (2000)

This paper looks at dynamic route guidance systems in terms of their use and trends. Two uses for dynamic route guidance are identified and their methods for calculating routes are described. Advantages and disadvantages of the two methods are discussed. The referencing method used by the two systems is described, particularly in terms of how it bridges the differences in accuracy, completeness, and the availability of current information.
Monitoring immunotherapy response in non-small cell lung cancer patients using 5-hydroxymethylcytosine signatures in circulating cell free DNA. (2020)

e21505 Background: Liquid biopsies are gaining prominence for not only cancer diagnosis but also patient monitoring. Mutational signals derived from cell-free DNA (cfDNA) show promise to assess response to cancer treatment, including immunotherapy. However, reliance of these methods on mutational data from tissue biopsies limit their applicability when a tumor biopsy is unavailable, or when mutational landscape of tumor changes under the selective pressures of cancer drug treatment. Epigenomic approaches have the potential to address these shortcomings. Methods: Blood draws were obtained from a cohort of non-small cell lung cancer (NSCLC) patients (n = 19) who went on to anti-PD1 treatment prior to therapy start and while on therapy. cfDNA was isolated from plasma and was subsequently processed to generate 5hmC genome-wide profiles. Results: We analyzed cfDNA from NSCLC patients undergoing anti-PD1 therapy to investigate whether immunotherapy response can be detected from plasma. Using a predictive model trained on lung cancer and non-cancer samples, we were able to detect changes in prediction scores in patient treated with immunotherapy that were consistent with RECIST. Patients with progressive disease (n = 3), determined by RECIST, had prediction scores that increased while they received treatment. On the other hand, majority of the patients that exhibited partial response to treatment (n = 12) had predictive scores that decreased with treatment, again consistent with RECIST. Furthermore, score changes consistent with RECIST was observed one cycle prior to the RECIST timepoint in all except one patient, where an extra blood draw after baseline was available (n = 7). Annotation of the regions that account for differential scoring identified enhancer, 5’UTR and promoter regions. Comparison of partial responders to patients with progressive disease revealed genes involved in metastasis, oncogenes and tumor suppressors that change in opposing directions between these patient groups, consistent with the underlying biology. Conclusions: Our results suggest that 5hmC profiles from cfDNA can be used to determine immunotherapy response in non-small cell lung cancer patients. Compared with mutation based liquid biopsy methods to assess response, epigenomics-based methods have the advantage of being agnostic to starting tumor mutations, and not relying on a mutational analysis from tumor biopsy. Future work will help determine applicability of this method to other kinds of therapies and cancer types.