gebhart/patrepeval huggingface dataset:
Multiple compartments with different metabolic characteristics are involved in biosynthesis of intracellular and released glutamine and citrate in astrocytes (2001)

The metabolism of glucose and lactate was investigated in cultured mouse cerebellar astrocytes, a culture preparation consisting of a homogeneous population of cells, by incubating the cells in a medium containing either [U-(13)C]glucose or [U-(13)C]lactate in combination with unlabeled lactate and glucose, respectively. After the incubation, cell extracts and media were analyzed by GC/MS (gas chromatography/mass spectrometry) for labeling patterns in aspartate, glutamate, and glutamine, as well as the tricarboxylic acid (TCA) cycle constituents citrate and fumarate. Triple labeling of extracellular citrate exceeded that of double labeling from [U-(13)C]glucose. This was not the case when lactate was the labeled precursor. These results indicate that pyruvate carboxylation in biosynthesis of releasable citrate was less prominent from lactate compared with glucose. As observed in the case of extracellular citrate, triple labeling of intracellular aspartate was higher than double labeling when [U-(13)C]glucose was the precursor, but not with [U-(13)C]lactate as precursor. The pattern of labeling in citrate was different intra- and extracellularly and the extent of labeling extracellularly was 10 times higher using [U-(13)C]glucose compared with [U-(13)C]lactate. However, the intracellular citrate labeling from [U-(13)C]glucose only exceeded that originating from labeled lactate by a factor of two. This is in contrast to the labeling pattern obtained for glutamine, since intracellularly this was equally prominent using [U-(13)C]glucose and [U-(13)C]lactate as substrates. Moreover, extracellularly the labeling was only slightly higher when using [U-(13)C]glucose compared with [U-(13)C]lactate. Intracellular glutamate and extracellular glutamine exhibited similar incorporation patterns with regard to double compared with triple labeling and the extent of incorporation of label from [U-(13)C]lactate compared with [U-(13)C]glucose. It should be noted that the main intracellular pools of citrate and glutamine were compartmentalized; i.e., releasable citrate and glutamine exhibited a labeling pattern distinctly different from that of their intracellular pools. Moreover, carboxylation of pyruvate using glucose as the precursor was more important for biosynthesis of releasable glutamine and citrate, compared with their intracellular pools. Based on the results a model of multiple compartments is suggested. The compartments differ with regard to utilization of lactate and glucose, synthetic pathways for TCA cycle intermediates and amino acids, particularly citrate and glutamine, as well as the contents of different metabolites.
A Comparison of Two Approaches for Vision and Self-Localization on a Mobile Robot (2007)

This paper considers two approaches to the problem of vision and self-localization on a mobile robot. In the first approach, the perceptual processing is primarily bottom-up, with visual object recognition entirely preceding localization. In the second, significant top-down information is incorporated, with vision and localization being intertwined. That is, the processing of vision is highly dependent on the robot's estimate of its location. The two approaches are implemented and tested on a Sony Aibo ERS-7 robot, localizing as it walks through a color-coded test-bed domain. This paper's contributions are an exposition of two different approaches to vision and localization on a mobile robot, an empirical comparison of the two methods, and a discussion of the relative advantages of each method.
Inhibition of PC‐3 human prostate cancers by analogs of growth hormone‐releasing hormone (GH‐RH) endowed with vasoactive intestinal peptide (VIP) antagonistic activity (2002)

Vasoactive intestinal peptide (VIP) stimulates the proliferation and invasiveness of malignant prostatic cells. Receptors for VIP and the closely related growth hormone-releasing hormone (GH-RH) show considerable homology and are found in prostatic and other carcinomas. Among various analogs of GH-RH synthesized, JV-1-52 is a non-selective VIP/GH-RH antagonist, whereas JV-1-53 is a VIP antagonist devoid of GH-RH antagonistic effect. In our study, nude mice bearing PC-3 human androgen-independent prostate carcinomas were treated with JV-1-52 or JV-1-53 (20 microg/day, s.c.) for 28 days. Both antagonists produced a similar reduction in tumor volume (62-67%, p < 0.01) and tumor weight (59-62%; p < 0.05) vs. controls and extended tumor doubling-time from 9.1 to about 16 days (p < 0.05). To investigate the mechanisms involved, in another study we compared the effects of JV-1-53 with those of somatostatin analog RC-160. VIP antagonist JV-1-53 reduced tumor weight by 67% (p < 0.01) and suppressed the expression of mRNA for c-fos and c-jun oncogenes by about 34% (p < 0.05), without affecting serum levels of insulin-like growth factor-I (IGF-I). In contrast, RC-160 (50 microg/day) reduced serum IGF-I by 19% (p < 0.05), but did not significantly decrease tumor weight. mRNA for VIP and high affinity receptors for VIP were detected on PC-3 tumors. Our results suggest that VIP/GH-RH antagonists can inhibit the growth of androgen-independent prostate cancer by abrogating the autocrine/paracrine mitogenic stimuli of VIP. The ability of GH-RH antagonists to block tumoral VIP receptors, in addition to GH-RH receptors, could be potentially beneficial for prostate cancer therapy.
Ubiquitous operating system (2011)

To enhance work efficiency by transforming public workstations into personal workstations where installed computer programs or files created in personal workstations can also be accessed at any public workstations. The&#13;\n&#13;\nrestriction of installing software in public workstations is common so as to prevent&#13;\n&#13;\nand protect the workstations from viruses or Trojans. Programs or files not found in&#13;\n&#13;\npublic workstations may forbid users from continuing with their work due to the&#13;\n&#13;\nincompatibility issue.
Engineering functional skin constructs: A quantitative comparison of three‐dimensional bioprinting with traditional methods (2021)

Tissue engineering has been successful in reproducing human skin equivalents while incorporating new approaches such as three-dimensional (3D) bioprinting. The latter method offers a plethora of advantages including increased production scale, ability to incorporate multiple cell types and printing on demand. However, the quality of printed skin equivalents compared to those developed manually has never been assessed. To leverage the benefits of this method, it is imperative that 3D-printed skin should be structurally and functionally similar to real human skin. Here, we developed four bilayered human skin epidermal-dermal equivalents: non-printed dermis and epidermis (NN), printed dermis and epidermis (PP), printed epidermis and non-printed dermis (PN), and non-printed epidermis and printed dermis (NP). The effects of printing induced shear stress [0.025 kPa (epidermis); 0.049 kPa (dermis)] were characterized both at the cellular and at the tissue level. At cellular level, no statistically significant differences in keratinocyte colony-forming efficiency (CFE) (p = 0.1641) were observed. In the case of fibroblasts, no significant differences in the cell alignment index (p < 0.1717) and their ability to contract collagen gel (p = 0.851) were detected. At the tissue levels, all the four skin equivalents were characterized using histological and immunohistochemical analysis with no significant differences found in either epidermal basal cell count, thickness of viable epidermis, and relative intensity of filaggrin and claudin-1. Our results demonstrated that 3D printing can achieve the same high-quality skin constructs as have been developed traditionally, thus opening new avenues for numerous high-throughput industrial and clinical applications.
KMT2C mutation associated with tumor mutational burden in small cell lung cancer. (2019)

e20098 Background: Immune checkpoint inhibitors are used to treat small cell lung cancer (SCLC). Tumor mutational burden (TMB) emerges as a promising predictor of immunotherapy efficacy, but the relationship between TMB and genetic features of SCLC remains unclear. In this study, we explored the correlation between genetic profiles and TMB in SCLC. Methods: FFPE tumor and matched blood samples were collected from 119 SCLC patients for panel targeted based next-generation sequencing. Genomic alterations (GAs) including single nucleotide variations, short and long insertions/deletions, copy number variations and gene rearrangements were assessed. Results: This study enrolled 114 SCLC and 5 mixed SCLC patients (91 males and 28 females) with a median age of 59 years. Median TMB was 9.3 muts/Mb (25% quantile: 6.3 muts/Mb, 75% quantile: 13.2 muts/Mb). For all patients, 31 (26%) had low TMB (≤6.3 muts/Mb), 55 (46%) had intermediate TMB (6.4-13.1 muts/Mb), and 33 (28%) had high TMB (≥13.2 muts/Mb). KMT2D mutations (mut), included substitution/indel (6/25) and truncation (19/25). KMT2D exhibited substitution/indel (6/25) and truncation (19/25) mutations in 19% of SCLC tumors while KMT2C exhibited substitution/indel (11/17), gene homozygous deletion (1/17) and truncation (5/17) mutations in 12% of SCLC tumors. Tumors with KMT family gene mut (KMT2C and KMT2D) (n = 33) had higher TMB (11.7 vs. 8.5 muts/Mb, p = 0.009). KMT2C mut tumors had higher TMB than KMT2C wildtype (wt) tumors (15.2 vs. 9.2 muts/Mb, p = 0.0036). TP53 mut occurred in 86% of KMT2C mut tumors and KMT2C/TP53 co-mutated tumors had higher TMB than KMT2C wt/TP53 mut tumors (17.8 vs. 9.3 muts/Mb, p = 0.0035) or KMT2C wt/TP53 wt tumors (17.8 vs. 5.4 muts/Mb, p = 0.027). Conclusions: Our data indicates that KMT family genes were frequently mutated in SCLC. KMT2C mut positively correlated with higher TMB and KMT2C co-mutated with TP53 or FAT1 may have a synergic effect on TMB. Our study explored a novel relationship between GAs and TMB that may greatly improve immunotherapeutic strategies for SCLC.
Alphaherpes viral genes and their functions (2007)

this chapter the emphasis is on viral replication and on the viral gene products that define the outcome of the interaction of the alphaherpesviruses with their host. Viral replicative and host management functions account for some of the RNAs and a large number of proteins encoded by the viruses. There are, however, numerous viral gene products whose functions have not been identified or which do not play a prominent role in viral replication in the systems in which these have been tested. The objective of the Table contained in this section is to summarize the functions of all known gene products and provide at least a few references for each product.
Carotid baroreflex responsiveness during dynamic exercise in humans (1993)

We utilized 5-s changes of neck pressure and neck suction (from 40 to -80 Torr) to alter carotid sinus transmural pressure in seven men with peak oxygen uptake (VO2peak) of 41.4 +/- 3.6 ml O2.kg-1.min-1. Peak responses of heart rate (HR) and mean arterial pressure (MAP) to each carotid sinus perturbation were used to construct open-loop baroreflex curves at rest and during exercise at 25.7 +/- 1.1 and 47.4 +/- 1.9% VO2peak. The baroreflex curves were fit to a logistic function describing the sigmoidal nature of the carotid sinus baroreceptor reflex. Maximal gain for baroreflex control of HR (-0.31 +/- 0.05 beats.min-1.mmHg-1) and MAP (-0.30 +/- 0.08 mmHg/mmHg) at rest was the same as during exercise at 25 and 50% VO2peak (-0.30 +/- 0.05, -0.39 +/- 0.13 beats.min-1.mmHg-1 for HR, P = NS; -0.23 +/- 0.04, -0.60 +/- 0.38 mmHg/mmHg for MAP, P = NS). Resetting of the baroreflex occurred during exercise at 50% VO2peak. The centering point, threshold, and saturation pressures were significantly increased for baroreflex control of HR (delta pressure = 26.3 +/- 6.8, 19.6 +/- 10.4, 33.0 +/- 5.6 mmHg, P < 0.05) and MAP (delta pressure = 27.1 +/- 7.7, 16.1 +/- 14.8, 38.2 +/- 8.5 mmHg, P < 0.05). The operating point (steady-state HR and MAP) was shifted closer to threshold of the baroreflex during exercise at 50% VO2peak, as reflected by differences in HR and MAP between the centering and operating points (delta HR = 12.5 +/- 4.7 beats/min, P = 0.10; delta MAP = 7.6 +/- 1.3 mmHg, P < 0.05). These findings suggest a resetting of the carotid baroreflex during exercise with no attenuation in maximal sensitivity. A shift in operating point toward threshold of the baroreflex enables effective buffering of elevations in systemic blood pressure via reflex alterations in HR and MAP.
Sphingosine-1–Phosphate Receptor–3 Is a Novel Biomarker in Acute Lung Injury (2012)

The inflamed lung exhibits oxidative and nitrative modifications of multiple target proteins, potentially reflecting disease severity and progression. We identified sphingosine-1-phosphate receptor-3 (S1PR3), a critical signaling molecule mediating cell proliferation and vascular permeability, as a nitrated plasma protein in mice with acute lung injury (ALI). We explored S1PR3 as a potential biomarker in murine and human ALI. In vivo nitrated and total S1PR3 concentrations were determined by immunoprecipitation and microarray studies in mice, and by ELISA in human plasma. In vitro nitrated S1PR3 concentrations were evaluated in human lung vascular endothelial cells (ECs) or within microparticles shed from ECs after exposure to barrier-disrupting agonists (LPS, low-molecular-weight hyaluronan, and thrombin). The effects of S1PR3-containing microparticles on EC barrier function were assessed by transendothelial electrical resistance (TER). Nitrated S1PR3 was identified in the plasma of murine ALI and in humans with severe sepsis-induced ALI. Elevated total S1PR3 plasma concentrations (> 251 pg/ml) were linked to sepsis and ALI mortality. In vitro EC exposure to barrier-disrupting agents induced S1PR3 nitration and the shedding of S1PR3-containing microparticles, which significantly reduced TER, consistent with increased permeability. These changes were attenuated by reduced S1PR3 expression (small interfering RNAs). These results suggest that microparticles containing nitrated S1PR3 shed into the circulation during inflammatory lung states, and represent a novel ALI biomarker linked to disease severity and outcome.
Analysis of periodontal risk profiles in adults with or without a history of myocardial infarction (2003)

The combination of five periodontal parameters in a PPRD added predictive value, suggesting that comprehensive data should be used in studies of associations between periodontitis and heart diseases. Radiographic evidence of bone loss was the best individual parameter.
Computation offloading for real-time health-monitoring devices (2016)

Among the major challenges in the development of real-time wearable health monitoring systems is to optimize battery life. One of the major techniques with which this objective can be achieved is computation offloading, in which portions of computation can be partitioned between the device and other resources such as a server or cloud. In this paper, we describe a novel dynamic computation offloading scheme for real-time wearable health monitoring devices that adjusts the partitioning of data between the wearable device and mobile application as a function of desired classification accuracy.
Source positioning in a large-scale tiny-sensor network of arbitrary topology (2014)

To effectively localise a source node in a dense wireless tiny-sensor network with an arbitrary 2D/3D node distribution, a novel approach suitable to describe the hop progress of source-to-sink path in such a system is proposed. In this approach, the network topology is described as a regular lattice and relates the statistical parameters of the hop count in the source-to-sink propagation path to the fractal properties of a percolating cluster. Based on this approach, a mathematical model is developed to estimate the probability P(r,t) of successful reception of the message by a sink node spaced at distance r from a source in a given time t. The accuracy analysis of the positioning method demonstrates its high performance for the very broad spectrum of values of the occupation probability pocc.
Discovery of Boceprevir and Narlaprevir: A Case Study for Role of Structure‐Based Drug Design (2012)

This chapter contains sections titled: List of Abbreviations References
DPWM Time Resolution Requirements for Digitally Controlled DC-DC Converters (2006)

Digitally controlled dc-dc converters can exhibit undesired limit-cycle oscillations due to the lack of time resolution in the digital pulse-width modulator (DPWM) to satisfy specified output voltage regulation accuracy. In this paper, the relationship between DPWM time resolution and output voltage regulation accuracy is studied for several basic converters operating in both continuous conduction mode (CCM) and discontinuous conduction mode (DCM). The minimum DPWM time resolution required to prevent limit-cycle oscillations is then derived cycle-skip, a technique for adjusting the switching frequency and on-time without load current sensing, is proposed to improve the output voltage regulation accuracy and lower DPWM resolution requirements. Experimental results are provided to validate the theoretical analysis and the effectiveness of the cycle-skip technique in avoiding limit-cycle oscillations.
Reduction of electromagnetic radiation from GSM mobile phone on human brain by the use of Bluetooth headset and earphone (2015)

Technology is considered to be the mount to climb up and attain the desired degree of development in a society. Man has been trying to facilitate his life through inventions and innovation. He invaded telecommunication system which leads to invention of mobile phones. In recent years, usage of mobile phone increased drastically. Since the mobile phone comes close to the head, concern about adverse effects of mobile phone radiation on the nervous system increased and this badly affects the human brain. This paper discussed on the analysis done to study the reduced effect of electromagnetic radiation on human brain from mobile phone when we used Bluetooth headset and earphone. The experiment was conducted in a laboratory using five volunteers. The mobile phone used is consist of GSM 2G technology. The period of operation is 10 minutes as talking time on the phone. Electroencephalogram is method which is used to monitor and capture the brain signals during the experimental analysis for 10 minutes interval. The result shows that the effects of electromagnetic radiations are reduced more for earphone use than the Bluetooth headset.
The Ubiquitin Ligase RNF220 Enhances Canonical Wnt Signaling through USP7-Mediated Deubiquitination of β-Catenin (2014)

Wnt/β-catenin signaling plays critical roles in embryonic development and disease. Here, we identify RNF220, a RING domain E3 ubiquitin ligase, as a new regulator of β-catenin. RNF220 physically interacts with β-catenin, but instead of promoting its ubiquitination and proteasomal degradation, it stabilizes β-catenin and promotes canonical Wnt signaling. Our analysis showed that RNF220 interacts with USP7, a ubiquitin-specific peptidase, which is required for RNF220 to stabilize β-catenin. The RNF220/USP7 complex deubiquitinates β-catenin and enhances canonical Wnt signaling. Interestingly, the stability of RNF220 itself is negatively regulated by Gsk3β, which is a key component of the β-catenin destruction complex and is inhibited upon Wnt stimulation. Accordingly, the RNF220/USP7 complex works as a positive feedback regulator of β-catenin signaling. In colon cancer cells with stimulated Wnt signaling, knockdown of RNF220 or USP7 impairs Wnt signaling and expression of Wnt target genes, suggesting a potentially novel role of RNF220 in Wnt-related tumorigenesis.
Cooperative Activation of TLR2 and Bradykinin B2 Receptor Is Required for Induction of Type 1 Immunity in a Mouse Model of Subcutaneous Infection by Trypanosoma cruzi (2006)

We have previously reported that exogenous bradykinin activates immature dendritic cells (DCs) via the bradykinin B(2) receptor (B(2)R), thereby stimulating adaptive immunity. In this study, we show that these premises are met in a model of s.c. infection by Trypanosoma cruzi, a protozoan that liberates kinins from kininogens through its major protease, cruzipain. Intensity of B(2)R-dependent paw edema evoked by trypomastigotes correlated with levels of IL-12 produced by CD11c(+) dendritic cells isolated from draining lymph nodes. The IL-12 response induced by endogenously released kinins was vigorously increased in infected mice pretreated with inhibitors of angiotensin converting enzyme (ACE), a kinin-degrading metallopeptidase. Furthermore, these innate stimulatory effects were linked to B(2)R-dependent up-regulation of IFN-gamma production by Ag-specific T cells. Strikingly, the trypomastigotes failed to up-regulate type 1 immunity in TLR2(-/-) mice, irrespective of ACE inhibitor treatment. Analysis of the dynamics of inflammation revealed that TLR2 triggering by glycosylphosphatidylinositol-anchored mucins induces plasma extravasation, thereby favoring peripheral accumulation of kininogens in sites of infection. Further downstream, the parasites generate high levels of innate kinin signals in peripheral tissues through the activity of cruzipain. The demonstration that the deficient type 1 immune responses of TLR2(-/-) mice are rescued upon s.c. injection of exogenous kininogens, along with trypomastigotes, supports the notion that generation of kinin "danger" signals is intensified through cooperative activation of TLR2 and B(2)R. In summary, we have described a s.c. infection model where type 1 immunity is vigorously up-regulated by bradykinin, an innate signal whose levels in peripheral tissues are controlled by an intricate interplay of TLR2, B(2)R, and ACE.
TANTIGEN 2.0: an online database and analysis platform for tumor T cell antigens (2019)

We previously developed TANTIGEN, a comprehensive web-based database cataloging more than 1,000 T cell epitopes and HLA ligands from 292 tumor antigens. TANTIGEN 2.0 is significantly expanded the number and coverage of immune response targets (T cell epitopes and HLA ligands) of previously cataloged tumor antigens. We expanded the number of cataloged tumor antigens to more than 4,000 and have added their reported targets of immune responses. We also included neoantigens, a new class of tumor antigens generated through mutations that results in a new amino acid sequence in tumor antigens. TANTIGEN 2.0 contains validated TCR sequences specific for cognate T cell epitopes. Gene expression information was extracted from tumor antigen gene/mRNA/protein expression information in major human cancers provided by Human Pathology Atlas. TANTIGEN 2.0 provides a rich data resource for tumor-associated epitope and neoepitope discovery studies. It is freely available at http://projects.met-hilab.org/tadb.
Radiotherapy for subfoveal neovascularisation associated with pathological myopia: a pilot study (2000)

Radiotherapy appeared to have a favourable treatment effect in eyes with subfoveal neovascular membranes and haemorrhage associated with pathological myopia. Further investigation is needed to evaluate the efficacy of radiotherapy for subfoveal neovascularisation associated with pathological myopia.