gebhart/patrepeval huggingface dataset:
Identification and Characterization of Vitamin A-Storing Cells in Fetal Liver: Implications for Functional Importance of Hepatic Stellate Cells in Liver Development and Hematopoiesis (2007)

Hepatic stellate cells (HpSTCs) are major regulators of hepatic fibrogenesis in adults. However, their early development in fetal liver is largely unknown. To characterize fetal HpSTCs in the liver, in which hepatic development and hematopoiesis occur in parallel, we determined the phenotypic characteristics of HpSTCs from rat fetal livers, using a strategy focused on vitamin A. Storage of vitamin A in the cytoplasm is a unique characteristic of HpSTCs, permitting identification of them by vitamin A-specific autofluorescence (vA+) when excited with UV light using flow cytometry. A characteristic vA+ cell population was identified in liver as early as 13 days post coitum; it had a surface phenotype of RT1A- intercellular adhesion molecule (ICAM)-1+ vascular cell adhesion molecule (VCAM)-1+ beta3-integrin+. Although nonspecific autofluorescent cells were found with the antigenic profile of RT1A- ICAM-1+ VCAM-1+, they were beta3-integrin- and proved to be hepatoblasts, bipotent hepatic parenchymal progenitors. In addition to expression of classic HpSTC markers, the vA+ cells were able to proliferate continuously in a serum-free hormonally defined medium containing leukemia inhibitory factor, which was found to be a key factor for their replication. These results demonstrated that the vA+ cells are fetal HpSTCs with extensive proliferative activity. Furthermore, the vA+ cells strongly express hepatocyte growth factor, stromal-derived factor-1alpha, and Hlx (homeobox transcription factor), indicating that they play important roles for hepatic development and hematopoiesis. The abilities to isolate and expand fetal HpSTCs enable further investigation into their roles in early liver development and facilitate identification of possibly novel signals of potential relevance for liver diseases.
VLSI issues in memory-system design for video signal processors (2002)

This paper addresses the design of memory-system architectures for video signal processors. The memory subsystem is the bottleneck of most video computing systems and demands a careful analysis of the design tradeoffs related to area, cycle time, and utilization. We emphasize the need to consider technological and circuit-level issues during the design of a system architecture, particularly that of a video processor, and present a method whereby the conceptual organization of the memory architecture can be evaluated before a detailed design is undertaken. Our analysis suggests that the organization of an efficient memory hierarchy for video signal processors is different from the register-cache based hierarchy of general-purpose programmable microprocessors.
Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway (2003)

RNA interference (RNAi), mediated by either long double-stranded RNA (dsRNA) or short interfering RNA (siRNA), has become a routine tool for transient knockdown of gene expression in a wide range of organisms. The antisense strand of the siRNA duplex (antisense siRNA) was recently shown to have substantial mRNA depleting activity of its own. Here, targeting human Tissue Factor mRNA in HaCaT cells, we perform a systematic comparison of the activity of antisense siRNA and double-strand siRNA, and find almost identical target position effects, appearance of mRNA cleavage fragments and tolerance for mutational and chemical backbone modifications. These observations, together with the demonstration that excess inactive double-strand siRNA blocks antisense siRNA activity, i.e. shows sequence-independent competition, indicate that the two types of effector molecules share the same RNAi pathway. Interest ingly, both FITC-tagged and 3'-deoxy antisense siRNA display severely limited activity, despite having practically wild-type activity in a siRNA duplex. Finally, we find that maximum depletion of target mRNA expression occurs significantly faster with antisense siRNA than with double-strand siRNA, suggesting that the former enters the RNAi pathway at a later stage than double-strand siRNA, thereby requiring less time to exert its activity.
Cannabinoid receptor 2 agonist ameliorates mesenteric angiogenesis and portosystemic collaterals in cirrhotic rats (2012)

CB(2) agonist alleviates portal hypertension (PH), severity of portosystemic collaterals and mesenteric angiogenesis, intrahepatic angiogenesis, and fibrosis in cirrhotic rats. The mechanism is, at least partly, through COX and NOS down-regulation. CBs may be targeted in the control of PH and portosystemic collaterals.
Crop Improvement through Modification of the Plant's Own Genome (2004)

Plant genetic engineering has, until now, relied on the incorporation of foreign DNA into plant genomes. Public concern about the extent to which transgenic crops differ from their traditionally bred counterparts has resulted in molecular strategies and gene choices that limit, but not eliminate, the introduction of foreign DNA. Here, we demonstrate that a plant-derived (P-) DNA fragment can be used to replace the universally employed Agrobacterium transfer (T-) DNA. Marker-free P-DNAs are transferred to plant cell nuclei together with conventional T-DNAs carrying a selectable marker gene. By subsequently linking a positive selection for temporary marker gene expression to a negative selection against marker gene integration, 29% of derived regeneration events contain P-DNA insertions but lack any copies of the T-DNA. Further refinements are accomplished by employing Omega-mutated virD2 and isopentenyl transferase cytokinin genes to impair T-DNA integration and select against backbone integration, respectively. The presented methods are used to produce hundreds of marker-free and backbone-free potato (Solanum tuberosum) plants displaying reduced expression of a tuber-specific polyphenol oxidase gene in potato. The modified plants represent the first example of genetically engineered plants that only contain native DNA.
Adding pyrrolysine to the Escherichia coli genetic code (2007)

Pyrrolysyl-tRNA synthetase and its cognate suppressor tRNA(Pyl) mediate pyrrolysine (Pyl) insertion at in frame UAG codons. The presence of an RNA hairpin structure named Pyl insertion structure (PYLIS) downstream of the suppression site has been shown to stimulate the insertion of Pyl in archaea. We study here the impact of the presence of PYLIS on the level of Pyl and the Pyl analog N-epsilon-cyclopentyloxycarbonyl-l-lysine (Cyc) incorporation using a quantitative lacZ-luc tandem reporter system in an Escherichia coli context. We show that PYLIS has no effect on the level of neither Pyl nor Cyc incorporation. Exogenously supplying our reporter system with d-ornithine significantly increases suppression efficiency, indicating that d-ornithine is a direct precursor to Pyl.
Lack of Benefit of Early Protocol Biopsies in Renal Transplant Patients Receiving TAC and MMF: A Randomized Study (2007)

We conducted a randomized, multicenter study to determine whether treatment of subclinical rejection with increased corticosteroids resulted in beneficial outcomes in renal transplant patients receiving tacrolimus (TAC), mycophenolate mofetil (MMF) and prednisone. One hundred and twenty-one patients were randomized to biopsies at 0,1,2,3 and 6 months (Biopsy arm), and 119 to biopsies at 0 and 6 months only (Control arm). The primary endpoint of the study was the prevalence of the sum of the interstitial and tubular scores (ci + ct)> 2 (Banff) at 6 months. Secondary endpoints included clinical and subclinical rejection and renal function. At 6 months, 34.8% of the Biopsy and 20.5% of the Control arm patients had a ci + ct score >or= 2 (p = 0.07). Between months 0 and 6, clinical rejection episodes were 12 in 10 Biopsy arm patients and 8 in 8 Control arm patients (p = 0.44). Overall prevalence of subclinical rejection in the Biopsy arm was 4.6%. Creatinine clearance at 6 months was 72.9 +/- 21.7 in the Biopsy and 68.90 mL/min +/- 18.35 mL/min in the Control arm patients (p = 0.18). In conclusion, we found no benefit to the procurement of early protocol biopsies in renal transplant patients receiving TAC, MMF and prednisone, at least in the short term. This is likely due to their low prevalence of subclinical rejection.
Comparative Effect of Transient Global Ischemia on Extracellular Levels of Glutamate, Glycine, and γ‐Aminobutyric Acid in Vulnerable and Nonvulnerable Brain Regions in the Rat (1991)

We evaluated whether regional differences in the magnitude of glutamate, gamma-aminobutyric acid (GABA), and glycine release could explain why some regions are vulnerable to ischemia whereas others are spared. By means of the microdialysis technique, the temporal profile of ischemia-induced changes in extracellular levels of glutamate, GABA, and glycine was compared in regions that demonstrate differing susceptibilities to a 10- and 20-min ischemic insult (dorsal hippocampus, anterior thalamus, somatosensory cortex, and dorsolateral striatum). The degree of ischemia (as established by local cerebral blood flow reduction) and the magnitude of histopathological neuronal damage were also evaluated in these regions. The blood flow reduction was severe and uniform in all regions; however, the histopathological outcome illustrated a different pattern. Whereas the CA1 sector of the hippocampus was severely damaged, the thalamus and cortex were relatively spared from both 10 and 20 min of ischemia. Striatal neurons were resistant to a 10-min insult but severely damaged after 20 min of ischemia. Ischemia-induced increase in glutamate and GABA content were of a similar magnitude and temporal profile in all four brain regions. A uniform increase in extracellular glycine levels was also observed in all four brain structures. The postischemic response, however, was different. Glycine levels remained twofold higher than baseline in the hippocampus but fell to baseline in the cortex and thalamus after both 10- and 20-min insults. In the striatum, glycine levels returned to baseline after 10 min of ischemia but remained relatively high after a 20-min insult.(ABSTRACT TRUNCATED AT 250 WORDS)
Optical Quantification of Cellular Mass, Volume, and Density of Circulating Tumor Cells Identified in an Ovarian Cancer Patient (2012)

Clinical studies have demonstrated that circulating tumor cells (CTCs) are present in the blood of cancer patients with known metastatic disease across the major types of epithelial malignancies. Recent studies have shown that the concentration of CTCs in the blood is prognostic of overall survival in breast, prostate, colorectal, and non-small cell lung cancer. This study characterizes CTCs identified using the high-definition (HD)-CTC assay in an ovarian cancer patient with stage IIIC disease. We characterized the physical properties of 31 HD-CTCs and 50 normal leukocytes from a single blood draw taken just prior to the initial debulking surgery. We utilized a non-interferometric quantitative phase microscopy technique using brightfield imagery to measure cellular dry mass. Next we used a quantitative differential interference contrast microscopy technique to measure cellular volume. These techniques were combined to determine cellular dry mass density. We found that HD-CTCs were more massive than leukocytes: 33.6 ± 3.2 pg (HD-CTC) compared to 18.7 ± 0.6 pg (leukocytes), p < 0.001; had greater volumes: 518.3 ± 24.5 fL (HD-CTC) compared to 230.9 ± 78.5 fL (leukocyte), p < 0.001; and possessed a decreased dry mass density with respect to leukocytes: 0.065 ± 0.006 pg/fL (HD-CTC) compared to 0.085 ± 0.004 pg/fL (leukocyte), p < 0.006. Quantification of HD-CTC dry mass content and volume provide key insights into the fluid dynamics of cancer, and may provide the rationale for strategies to isolate, monitor or target CTCs based on their physical properties. The parameters reported here can also be incorporated into blood cell flow models to better understand metastasis.
LSTM: A Search Space Odyssey (2016)

Several variants of the long short-term memory (LSTM) architecture for recurrent neural networks have been proposed since its inception in 1995. In recent years, these networks have become the state-of-the-art models for a variety of machine learning problems. This has led to a renewed interest in understanding the role and utility of various computational components of typical LSTM variants. In this paper, we present the first large-scale analysis of eight LSTM variants on three representative tasks: speech recognition, handwriting recognition, and polyphonic music modeling. The hyperparameters of all LSTM variants for each task were optimized separately using random search, and their importance was assessed using the powerful functional ANalysis Of VAriance framework. In total, we summarize the results of 5400 experimental runs ( ≈ 15 years of CPU time), which makes our study the largest of its kind on LSTM networks. Our results show that none of the variants can improve upon the standard LSTM architecture significantly, and demonstrate the forget gate and the output activation function to be its most critical components. We further observe that the studied hyperparameters are virtually independent and derive guidelines for their efficient adjustment.
The Role of Peripheral Nerve Surgery in the Management of Painful Chronic Wounds: Indications and Outcomes (2008)

This study suggests that an additional treatment modality in the management of chronic wounds can be considered for patients with disabling pain. As an adjunct to other interventions, this novel application of peripheral nerve surgery can critically improve symptoms in selected patients with intractable chronic wound pain.
Compact differential InP-based HBT VCO's with a wide tuning range at W-band (2002)

Compact monolithic integrated differential VCO's operating in W-band were realized using InP-based HBT's. The oscillators, with a total chip size of 0.6 mm by 0.35 mm, are based on a balanced Colpitts-type topology with a coplanar transmission line resonator. By varying the voltage across the base-collector junction of the HBT in the current mirror and by changing the current in the VCO, the oscillation frequency can be tuned between 84 and 106 GHz. At 100 GHz, a differential voltage swing of 400 mV is obtained, which should be sufficient to drive 100 Gb/s digital logic.
Properties of Fluorescent Semiconductor Nanocrystals and their Application to Biological Labeling (2001)

We review recent advances in the development of colloidal fluorescent semiconductor nanocrystals (a class of quantum dots) for biological labeling. Although some of the photophysical properties of nanocrystals are not fully understood and are still actively investigated, researchers have begun developing bioconjugation schemes and applying such probes to biological assays. Nanocrystals possess several qualities that make them very attractive for fluorescent tagging: broad excitation spectrum, narrow emission spectrum, precise tunability of their emission peak, longer fluorescence lifetime than organic fluorophores and negligible photobleaching. On the down side, their emission is strongly intermittent (“blinking”) and their size is relatively large for many biological uses. We describe how to take advantage of nanocrystals' spectral properties to increase the resolution of fluorescence microscopy measurements down to the nanometer level. We also show how their long fluorescence lifetime can be used to observe molecules and organelles in living cells without interference from background autofluorescence, a pre-requisite for single molecule detectability. Finally, their availability in multicolor species and their single molecule sensitivity open up interesting possibilities for genomics applications.
A complexomic study of Escherichia coli using two‐dimensional blue native/SDS polyacrylamide gel electrophoresis (2006)

Study of the complexome - all the protein complexes of the cell - is essential for a better understanding and more global vision of cell function. Using two-dimensional blue native/SDS-PAGE (2-D BN/SDS-PAGE) technology, the cytosolic and membrane protein complexes of Escherichia coli were separated. Then, the different partners of each protein complex were identified by LC-MS/MS. In this report, 306 protein complexes were separated and identified. Among these protein complexes, 50 heteromultimeric and 256 homomultimeric protein complexes were found. Among the 50 heteromultimeric protein complexes, 18 previously described protein complexes validate the technology. In this study, 109 new protein complexes were found, providing insight into the function of previously uncharacterized bacterial proteins.
Switchable Bragg gratings based on soft materials (2006)

Topic of the thesis is the study of diffraction Bragg gratings holographically recorded in polymer-liquid crystal composite materials. Due to the special electro-optical properties of liquid crystals, these gratings can be electrically driven, switching between a diffraction and a transmission state. In the present work, techniques and materials used to produce such gratings are described, with emphasis on the connections between the final morphology and the preparation procedure, materials and exposure. Different types of gratings have been characterized, both in the visible and in the near infrared range, in view of a possible use as photonic devices in the optical communication systems. Grating diffraction efficiency has been measured varying the wavelength, the temperature, the angle of incidence and the applied electric field. The behavior in dynamic conditions has been analyzed by measuring switching times for electric pulse of variable amplitude and duration. These measurements have been analyzed with suitable mathematical models and related to the morphology of the studied materials, like the interface between polymer and liquid crystal, anisotropy of liquid crystal domains and the degree of phase separation. Results obtained provide a deeper insight into the structure of such materials and make possible the optimization of their properties and the design of different photonic devices. Finally, the use of variable angle ellipsometry and /or half-leaky guide mode technique to measure soft material optical properties is discussed.
SNIPER(TACC3) induces cytoplasmic vacuolization and sensitizes cancer cells to Bortezomib (2017)

We previously developed a hybrid small molecule SNIPER (Specific and Nongenetic IAP-dependent Protein ERaser) against transforming acidic coiled-coil-3 (TACC3), SNIPER(TACC3), that induces proteasomal degradation of TACC3 protein. In this study, we found that SNIPER(TACC3) induces cytoplasmic vacuolization derived from endoplasmic reticulum (ER) and paraptosis-like cell death selectively in cancer cells. Mechanistic analysis suggests that accumulation of ubiquitylated protein aggregates that requires X-linked inhibitor of apoptosis protein (XIAP) induces ER stress, which results in ER-stress responses involving X-box binding protein-1 (XBP-1) and ER-derived vacuolization in cancer cells. Importantly, inhibition of proteasome enhanced the SNIPER(TACC3)-induced vacuolization, and the combination treatment of SNIPER(TACC3) and bortezomib exhibited a synergistic anticancer activity in several cancer cell lines. The induction of paraptosis-like cell death in cancer cells by SNIPER(TACC3) could be applied to treat cancer cells resistant to undergo apoptosis by overexpression of XIAP.
Direct association of pp40/I kappa B beta with rel/NF-kappa B transcription factors: role of ankyrin repeats in the inhibition of DNA binding activity. (1992)

To understand the mechanism by which pp40/I kappa B beta inhibits DNA binding activity of the rel/NF-kappa B family of transcription factors, we have investigated the role of ankyrin repeats on the biological function of pp40 by deleting or mutating conserved residues. We show that (i) ankyrin repeats alone are not sufficient to manifest biological activity but require the C-terminal region of the pp40 protein; (ii) four out of the five ankyrin repeats are essential for inhibiting the DNA binding activity; (iii) pp40 mutants that do not inhibit DNA binding of rel protein also do not associate with rel; (iv) although pp40 can associate with the p65 and p50 subunits of NF-kappa B, pp40 inhibits the DNA binding activity of only the p50-p65 heterodimer and the p65 homodimer; and (v) pp40 inhibits the transcription of genes linked to kappa B site; however, mutants that do not affect DNA binding have no effect. We propose that the ankyrin repeats and the C-terminal region of pp40 form a structure that associates with the rel homology domain to inhibit DNA binding activity.
Resolution of the two components of macrophage inflammatory protein 1, and cloning and characterization of one of those components, macrophage inflammatory protein 1 beta. (1988)

A number of macrophage-derived mediators have been implicated in the vascular changes of inflammation. We recently reported the isolation of a novel monokine, macrophage inflammatory protein 1 (MIP-1), which causes local inflammatory responses in vivo, and induces superoxide production by neutrophils in vitro. Purified native MIP-1 comprises two peptides with very similar physical characteristics. We report here the resolution of MIP-1 into component peptides by SDS-hydroxylapatite chromatography, and compare the NH2-terminal sequences of the two peptides, now referred to as MIP-1 alpha and MIP-1 beta. A synthetic oligonucleotide probe pool corresponding to the NH2-terminal amino acid sequence of MIP-1 beta was used to isolate a cDNA clone containing its coding sequence. The sequence codes for a 109 amino acid-long polypeptide, of which 69 amino acids correspond to the mature product. Comparison of this MIP-1 beta cDNA with our previously cloned MIP-1 alpha sequence reveals that the MIP-1 peptides, members of a growing family of potential inflammatory mediators, are distinct but highly homologous (58.9% sequence identity) products of different genes.
N-terminal proatrial natriuretic factor. An independent predictor of long-term prognosis after myocardial infarction. (1994)

The measurement of N-terminal proANF supplements presently used clinical and objective assessments and provides an important independent predictor of prognosis with respect to cardiovascular mortality and development of heart failure.