gebhart/patrepeval huggingface dataset:
Phosphorylation status of pyruvate dehydrogenase distinguishes metabolic phenotypes of cultured rat brain astrocytes and neurons (2010)

Glucose metabolism in nervous tissue has been proposed to occur in a compartmentalized manner with astrocytes contributing largely to glycolysis and neurons being the primary site of glucose oxidation. However, mammalian astrocytes and neurons both contain mitochondria, and it remains unclear why in culture neurons oxidize glucose, lactate, and pyruvate to a much larger extent than astrocytes. The objective of this study was to determine whether pyruvate metabolism is differentially regulated in cultured neurons versus astrocytes. Expression of all components of the pyruvate dehydrogenase complex (PDC), the rate-limiting step for pyruvate entry into the Krebs cycle, was determined in cultured astrocytes and neurons. In addition, regulation of PDC enzymatic activity in the two cell types via protein phosphorylation was examined. We show that all components of the PDC are expressed in both cell types in culture, but that PDC activity is kept strongly inhibited in astrocytes through phosphorylation of the pyruvate dehydrogenase alpha subunit (PDH alpha). In contrast, neuronal PDC operates close to maximal levels with much lower levels of phosphorylated PDH alpha. Dephosphorylation of astrocytic PDH alpha restores PDC activity and lowers lactate production. Our findings suggest that the glucose metabolism of astrocytes and neurons may be far more flexible than previously believed.
Pharmacogenetic profiling of drug metabolizing enzyme genes (2005)

Background Pharmacogenetic testing has become increasingly important in drug development and pharmaco-vigilance processes. To understand the inter-individual differences in active pathways, tests that target multiple drug metabolizing and drug interacting proteins are required. Method A DNA microarray was developed that consists of an array-of arrays for genotyping 16 samples simultaneously (the DrugMEt™ Test). Genotyping is accomplished in a single reaction with allele-specific primers for 27 SNPs of eight highly polymorphic genes: CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, TPMT, NAT2, and MDR1. The accuracy and reproducibility were evaluated, and a method comparison with the TaqMan™ assay was performed. The applicability of the method was investigated with samples from different ethnic backgrounds. Results For the various SNPs, an accuracy >99%, and reproducibility of >95%, was observed. The method comparison indicated >95% concordance between the DrugMEt™ Test and TaqMan™ assay. The genotype frequencies of the Caucasian, African American, and Asian populations matched those published in the literature. Conclusions The multigene DrugMEt™ microarray provides a straight-forward basis for the selection of a drug compound for future development, and identification of the potential responder population. Moreover, drug-interacting pathways may be identified. Clinical Pharmacology & Therapeutics (2005) 77, P64–P64; doi: 10.1016/j.clpt.2004.12.135
Joint wireless information and energy transfer in cache-assisted relaying systems (2018)

We investigate the performance of time switching (TS) based energy harvesting model for cache-assisted simultaneous wireless transmission of information and energy (Wi-TIE). In the considered system, a relay which is equipped with both caching and energy harvesting capabilities helps a source to convey information to a destination. First, we formulate based on the time-switching architecture an optimization problem to maximize the harvested energy, taking into consideration the cache capability and user quality of service requirement. We then solve the formulated problem to obtain closed-form solutions. Finally, we demonstrate the effectiveness of the proposed system via numerical results.
Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2′,4,4′-tetrabromodiphenyl ether (2019)

2,2',4,4'-Tetrabromodiphenyl ether (BDE-47), a predominant polybrominated diphenyl ether (PBDE), has received extensive attention for its potential environmental impact. An integrated study of metabolomics and transcriptomics was conducted on two rice (Oryza sativa) cultivars, Lianjing-7 (LJ-7) and Yongyou-9 (YY-9), which have been identified as tolerant and sensitive cultivars to BDE-47, respectively. The objective was to investigate the molecular mechanisms of their different ability to tolerate BDE-47. Both rice plants were cultivated to maturity in soils containing three concentrations of BDE-47 (10, 20, and 50 mg/kg). Metabolomic analyses of rice grains identified 65 metabolites in LJ-7 and 45 metabolites in YY-9, including amino acids, saccharides, organic acids, fatty acids, and secondary metabolites. In the tolerant cultivar LJ-7 exposed to 50 mg/kg BDE-47, concentrations of most of the metabolites increased significantly, with α-ketoglutaric acid increased by 20-fold and stigmastanol increased by 12-fold. In the sensitive cultivar YY-9, the concentrations of most metabolites increased after the plant was exposed to 1 and 10 mg/kg BDE-47 but decreased after the plant was exposed to 50 mg/kg BDE-47. Transcriptomic data demonstrated that regulation of gene expressions was affected most in LJ-7 exposed to 50 mg/kg BDE-47 (966 genes up-regulated and 620 genes down-regulated) and in YY-9 exposed to 10 mg/kg BDE-47 (85 genes up-regulated and 291 genes down-regulated), in good accordance with the observed metabolic alternation in the two cultivars. Analyses of metabolic pathways and KEGG enrichment revealed that many biological processes, including energy consumption and biosynthesis, were perturbed in the two rice cultivars by BDE-47. A majority of metabolites and genes involved in dominating pathways of energy consumption (e.g., tricarboxylic acid cycle) and the biosynthesis (e.g., metabolism of saccharides and amino acids) were enhanced in LJ-7 by BDE-47. In contrast, energy consumption was increased while biosynthetic processes were inhibited in YY-9 by BDE-47, which could lead to the sensitivity of YY-9 to BDE-47. The combined results suggest that the different defensive abilities of these two rice cultivars in response to BDE-47 could be attributed to their differences in energy-consumption strategy and biosynthesis of nutritional components in grains. This study provides a useful reference for rice cultivation in PBDE-polluted areas.
Studies on the Autonomic Nervous Function in Tsukuba Emotional Rats-with Special Reference to Their Cardiac Function. (1993)

Autonomic nervous function in Tsukuba high (THE) and low (TLE) emotional rats as well as Wistar rats (control) was studied by means of electrocardiographical examination in addition to the runway test. In the runway test, locomotive activity differed significantly among the three strains, the greatest activity in TLE and the smallest in THE. Electrocardiogram (ECG) and locomotive activity were successively recorded for 24 hr using a small size of telemeter system. Though the locomotive activity showed a clear nocturnal rhythm, no significant difference was observed among the three strains. The mean value of R-R intervals in THE tended to be smaller than those in other two strains; showing a significant difference between THE and TLE. The mean value of standard deviation (SD) of R-R intervals in TLE tended to be larger than those in other two strains; showing a significant difference between TLE and Wistar in the light and dark periods, and also between TLE and THE in the light period. As regards coefficients of variation of R-R intervals (CV), there was no significant difference among the three strains. Autonomic nervous tone in THE and TLE was evaluated by means of autonomic blockades using atropine and/or propranolol. The sympathetic nervous tone represented 21.6% in THE and 16.8% in TLE, while the parasympathetic nervous tone -9.0% and -12.3% in THE and TLE, respectively. There was a significant difference in the net autonomic nervous tone between THE (10.7%) and TLE (-6.6%).(ABSTRACT TRUNCATED AT 250 WORDS)
Document Classification and Page Stream Segmentation for Digital Mailroom Applications (2013)

In this paper we present a method for the segmentation of continuous page streams into multipage documents and the simultaneous classification of the resulting documents. We first present an approach to combine the multiple pages of a document into a single feature vector that represents the whole document. Despite its simplicity and low computational cost, the proposed representation yields results comparable to more complex methods in multipage document classification tasks. We then exploit this representation in the context of page stream segmentation. The most plausible segmentation of a page stream into a sequence of multipage documents is obtained by optimizing a statistical model that represents the probability of each segmented multipage document belonging to a particular class. Experimental results are reported on a large sample of real administrative multipage documents.
Dynamic remodeling of <i>Escherichia coli</i> interactome in response to environmental perturbations (2023)

Proteins play an essential role in the vital biological processes governing cellular functions. Most proteins function as members of macromolecular machines, with the network of interacting proteins revealing the molecular mechanisms driving the formation of these complexes. Profiling the physiology-driven remodeling of these interactions within different contexts constitutes a crucial component to achieving a comprehensive systems-level understanding of interactome dynamics. Here, we apply co-fractionation mass spectrometry and computational modeling to quantify and profile the interactions of ∼2000 proteins in the bacterium Escherichia coli cultured under 10 distinct culture conditions. The resulting quantitative co-elution patterns revealed large-scale condition-dependent interaction remodeling among protein complexes involved in diverse biochemical pathways in response to the unique environmental challenges. The network-level analysis highlighted interactome-wide biophysical properties and structural patterns governing interaction remodeling. Our results provide evidence of the local and global plasticity of the E. coli interactome along with a rigorous generalizable framework to define protein interaction specificity. We provide an accompanying interactive web application to facilitate the exploration of these rewired networks.
<i>Bacteroides Fragilis:</i> Current Susceptibilities, Mechanisms of Drug Resistance, and Principles of Antimicrobial Therapy (1986)

The Bacteroides fragilis group of organisms includes the most clinically important anaerobic bacteria. Optimal therapy of infections in which these organisms are involved includes adequate and timely surgical drainage of all collections, debridement of necrotic tissue, optimal nutritional support, and administration of appropriate empiric antibiotics to cover both the aerobic and anaerobic bacterial components of these mixed infections. Special attention must be paid to the B. fragilis group because of its high rate of resistance to many of the commonly used antibiotics. Of the currently available beta-lactam antibiotics, piperacillin has the lowest rate of resistance. Successful antimicrobial agents include clindamycin, chloramphenicol, and metronidazole plus an aminoglycoside. Piperacillin, cefoxitin, and moxalactam can be used with an aminoglycoside or alone if no resistant organisms are revealed on culture and susceptibility testing. Beta-lactam-based regimens are potentially less toxic and may be less costly than those that contain one or more non-beta-lactam antibiotics.
Blockade of sphingosine‐1‐phosphate reduces macrophage influx and retinal and choroidal neovascularization (2008)

Sphingosine-1-phosphate (S1P) is a bioactive lipid molecule that stimulates endothelial cell migration, proliferation, and survival in vitro, and tumor angiogenesis in vivo. In this study, we used a humanized monoclonal antibody (sonepcizumab) that selectively binds S1P to investigate its role in retinal and choroidal neovascularization (NV). Intraocular injection of sonepcizumab significantly reduced macrophage influx into ischemic retina and strongly suppressed retinal NV in mice with oxygen-induced ischemic retinopathy. In mice with laser-induced rupture sites in Bruch's membrane, intraocular injection of sonepcizumab significantly reduced the area of choroidal NV and concomitantly reduced fluorescein leakage from the remaining choroidal NV. Four weeks after intraocular injection of up to 1.8 mg of the sonepcizumab in non-human primates, electroretinograms and fluorescein angiograms were normal, and light microscopy of ocular sections showed no evidence of structural damage. These data show for the first time that S1P stimulates both choroidal and retinal NV and suggest that sonepcizumab could be considered for evaluation in patients with choroidal or retinal NV.
Stabilization of Volar Ulnar Rim Fractures of the Distal Radius: Current Techniques and Review of the Literature (2016)

Background Distal radius fractures involving the lunate facet can be challenging to manage. Reports have shown the volar carpal subluxation/dislocation that can occur if the facet is not appropriately stabilized. Literature Review Recent emphasis in the literature has underscored the difficulty in managing this fracture fragment, suggesting standard volar plates may not be able to adequately stabilize the fragment. This article reviews the current literature with a special emphasis on fixation with a specifically designed fragment-specific hook plate to secure the lunate facet. Case Description An extended flexor carpi radialis volar approach was made which allows access to the distal volar ulnar fracture fragment. Once provisionally stabilized with Kirschner wire fixation, a volar hook plate was applied to capture this fragment. Additional fracture stabilization was used as deemed necessary to stabilize the remaining distal radius fracture. Clinical Relevance The volar marginal rim fragment remains a challenge in distal radius fracture management. Use of a hook plate to address the volar ulnar corner allows for stable fixation without loss of reduction at intermediate-term follow-up.
Ultrafast computed tomography for quality control of automated proximal anastomoses. (2003)

The feasibility of proximal anastomoses using the Symmetry device has been reported. Patency control with invasive angiography has been performed by other groups. With MDCT, noninvasive evaluation of proximal anastomotic quality and graft patency is possible, even if nitinol is implanted.
Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen (2019)

The 16 diabetic kidney disease-associated loci may provide novel insights into the pathogenesis of this condition and help identify potential biologic targets for prevention and treatment.
Pixel-Parallel 3D Integrated CMOS Image Sensors Developed by Direct Bonding of SOI Layers for Next-Generation Video Systems (2018)

We report pixel-parallel 3D integrated CMOS image sensors with pulse-frequency-modulation A/D converters (ADCs). Direct bonding of silicon-on-insulator (SOI) wafers with Au electrodes embedded in a SiO2 intermediate layer provides pixel-wise interconnection in the sensor. Quarter video graphics array resolution sensors are developed from two SOI wafers, where photodiodes, logic circuits and 16-bit counters are integrated in every pixel. We have successfully captured video images of 16-bit digital signal and confirmed a wide dynamic range of 96 dB, indicating the feasibility of high-performance pixel-level imaging for next-generation image sensors.
Extremely low voltage organic light-emitting diodes with p-doped alpha-sexithiophene hole transport and n-doped phenyldipyrenylphosphine oxide electron transport layers (2006)

Organic light-emitting diodes with p-doped alpha-sexithiophene and n-doped phenyldipyrenylphosphine oxide carrier transport layers are fabricated. In the doped diodes, the authors demonstrate an extremely low driving voltage of 2.9V at a current density of 100mA∕cm2 and very high luminance at a low driving voltage: 1000cd∕m2 at 2.4V, 10000cd∕m2 at 2.8V, and 920000cd∕m2 at 4.5V. Such lowered driving voltages and enhanced luminance characteristics are attributed to the generation of free charge carriers by charge transfer from matrix to dopant molecules, resulting in an increase in electrical conductivities and formation of Ohmic contacts at metal/organic interfaces.
Phase II Trial of Tipifarnib plus Neoadjuvant Doxorubicin-Cyclophosphamide in Patients with Clinical Stage IIB-IIIC Breast Cancer (2009)

Tipifarnib inhibits FTase activity in human breast tumors in vivo, is associated with down-regulation of p-STAT3, and enhances the breast pCR rate, thus meriting further evaluation.
Absorption of NOx, SO2, and Mercury in a simulated additive-enhanced wet flue gas desulphurization scrubber (2010)

Bench- and pilot-scale studies were conducted on the simultaneous removals of SO2, NOx, and mercury (both Hg 0 and Hg 2+ ) from coal combustion flue gas using a limestone-based wet flue gas desulfurization (FGD) scrubber. The wet scrubber performance for multi-pollutant control was significantly enhanced with the introduction of an oxidizing additive – sodium chlorite (NaClO2). Parametric studies investigating the effects of flue gas components (e.g., SO2, NO), temperature, and oxidant addition rate were completed with the benchand pilot-scale experimental facilities. Various process configurations were examined to optimize the addition of sodium chlorite. Additional tests were also performed to better understand the chemistry of the oxidation and subsequent capture of the pollutants of interest.
The Results of Small Satellite Technology Transfer from JAXA (2010)

The satellite named MAIDO-1 finished its 9-month life, on October 15, 2009. The MAIDO-1 was developed by Space Oriented Higashiosaka Leading Association (SOHLA). Japan Aerospace Exploration Agency(JAXA) transferred their space technology to small and medium-sized enterprises (SMEs) and local universities in the Kansai area. The purpose of this activity is to contribute to socio-economic development by returning JAXA research and development results to society. The MAIDO-1 is one of its program achievements. This paper shall explain the matter of the technology transfer, the SOHLA-1 satellite system, on-orbit experimental results, and the results of technology transfers.
Supplementary Table 4A from Tumor Suppressor Functions of &lt;i&gt;ARLTS1&lt;/i&gt; in Lung Cancers (2023)

Supplementary Table 4A from Tumor Suppressor Functions of &lt;i&gt;ARLTS1&lt;/i&gt; in Lung Cancers
The use of stem cell assays to monitor the proliferative potential of bone marrow cells. (1979)

A number of assays exist for hematopoietic stem cells in both humans and mice, but the appropriate stem cell assay for the repopulating potential of human marrow is not clear. Two murine models suggest that these assays may not always predict marrow proliferative potential. In vivo diffusion chamber culture growth of CD1 marrow depleted of pluripotent stem cells (CFU-S) by exposure to mouse-brain antisera plus complement was equivalent to or greater than that of normal serum treated control marrow. Furthermore, CF1 mice repeatedly injected with endotoxin had markedly stimulated granulopoiesis with increases in the number of marrow CFU-S and the % in S phase but no changes in the number or proliferative status of marrow CFU-C. However, inbred BDF1 mice chronically injected with endotoxin although also showing striking increases in granulopoiesis had no significant alteration in their marrow CFU-S or CFU-C number or cell cycle status relative to saline injected controls. Both models present examples where conventional stem cell assays do not provide insight into marrow cell production and suggest that in vitro clonal assays of human marrow cells may not always predict for the potential of marrow to repopulate a human transplant recipient.
Supplementary Figure 4 from Humanization of an Anti-CCR4 Antibody That Kills Cutaneous T-Cell Lymphoma Cells and Abrogates Suppression by T-Regulatory Cells (2023)

&lt;p&gt;PDF file, 51K, CDC activity of h1567, 1-44 and 2-3 variants against Mac-1 cells.&lt;/p&gt;
Binding and regulation of thrombopoietin to human megakaryocytes (1998)

Thrombopoietin (TPO, c-Mpl ligand) is considered to play an important role in the regulation of megakaryocytopoiesis and platelet production by activating the cytokine receptor c-Mpl. We have examined the binding of 125I-TPO to the human megakaryocytic cell line, CMK, and to primary human megakaryocytes. Scatchard analysis of TPO binding to its cognate receptor in megakaryocytic cells suggested the existence of a single class of c-Mpl receptors. CMK cells exhibited 1223 receptors per cell with a dissociation constant (Kd) of Kd = 223 pM, whereas primary human megakaryocytes exhibited 12140 receptors per cell and a dissociation constant of Kd = 749 pM. The pretreatment of CMK cells and primary bone marrow megakaryocytes with TPO resulted in a decreased binding of TPO to the c-Mpl receptors. This down-regulation was observed within 3 h and was not inhibited by cycloheximide. Phorbol ester, an activator of protein kinase C, also inhibited TPO binding to the c-Mpl receptors by reducing the number of these receptors. The pretreatment of CMK cells with IL-3, IL-6 and DMSO, all of which induced the differentiation of CMK cells, did not affect the binding of TPO to the c-Mpl receptors. These results suggest an additional mechanism, where protein kinase C may help to regulate the binding of TPO to these cells.
A comparison of verification in the temporal and cepstrum-transformed domains of Transient Evoked Otoacoustic Emissions for biometric identification (2011)

An investigation of methods for the use of Transient Evoked Otoacoustic Emissions (TEOAE) as an identification biometric is described in this paper. Three methods to calculate the Euclidean distance between individuals are investigated: Interpretation of area-under-the-curve information from time-series TEOAE; Measurement in the temporal domain between a TEOAE and reference template; Measurement in the cepstral domain between a TEOAE and reference template. False acception and rejection rates (FAR&FRR) are given for test data. In this study maximal performance was given by the temporal domain Euclidian distance, giving 1.27%FAR and 0%FRR for a data set with 230 recordings from 23 subjects.