gebhart/patrepeval huggingface dataset:
Ga+beam lithography for nanoscale silicon reactive ion etching (2010)

By using a dry etch chemistry which relies on the highly preferential etching of silicon, over that of gallium (Ga), we show resist-free fabrication of precision, high aspect ratio nanostructures and microstructures in silicon using a focused ion beam (FIB) and an inductively coupled plasma reactive ion etcher (ICP-RIE). Silicon etch masks are patterned via Ga(+) ion implantation in a FIB and then anisotropically etched in an ICP-RIE using fluorinated etch chemistries. We determine the critical areal density of the implanted Ga layer in silicon required to achieve a desired etch depth for both a Pseudo Bosch (SF(6)/C(4)F(8)) and cryogenic fluorine (SF(6)/O(2)) silicon etching. High fidelity nanoscale structures down to 30 nm and high aspect ratio structures of 17:1 are demonstrated. Since etch masks may be patterned on uneven surfaces, we utilize this lithography to create multilayer structures in silicon. The linear selectivity versus implanted Ga density enables grayscale lithography. Limits on the ultimate resolution and selectivity of Ga lithography are also discussed.
Electrical modeling, simulation and SPICE model extraction of TSVs in silicon interposer (2011)

In this paper, electrical characteristic of TSV (Through Silicon Via) is analyzed. Firstly, equivalent circuit model of TSV is summarized. Modeling and electrical analysis of TSV is conducted, in which TSVs with ideal and non-ideal profiles are compared. And then, multi-TSV configuration in silicon interposer is modeled and analyzed. Capacitive and inductive coupling between TSVs are simulated. With these analyses, solutions to decrease crosstalk between TSVs are proposed.
GFP-like Proteins as Ubiquitous Metazoan Superfamily: Evolution of Functional Features and Structural Complexity (2004)

Homologs of the green fluorescent protein (GFP), including the recently described GFP-like domains of certain extracellular matrix proteins in Bilaterian organisms, are remarkably similar at the protein structure level, yet they often perform totally unrelated functions, thereby warranting recognition as a superfamily. Here we describe diverse GFP-like proteins from previously undersampled and completely new sources, including hydromedusae and planktonic Copepoda. In hydromedusae, yellow and nonfluorescent purple proteins were found in addition to greens. Notably, the new yellow protein seems to follow exactly the same structural solution to achieving the yellow color of fluorescence as YFP, an engineered yellow-emitting mutant variant of GFP. The addition of these new sequences made it possible to resolve deep-level phylogenetic relationships within the superfamily. Fluorescence (most likely green) must have already existed in the common ancestor of Cnidaria and Bilateria, and therefore GFP-like proteins may be responsible for fluorescence and/or coloration in virtually any animal. At least 15 color diversification events can be inferred following the maximum parsimony principle in Cnidaria. Origination of red fluorescence and nonfluorescent purple-blue colors on several independent occasions provides a remarkable example of convergent evolution of complex features at the molecular level.
Selective activation of particulate cAMP-dependent protein kinase by isoproterenol and prostaglandin E1. (1980)

Previously, we have found that in perfused rat hearts, isoproterenol and prostaglandin E1 (PGE1) caused comparable increases in CAMP and activations of protein kinase but that only isoproterenol led to the phosphorylation of several substrates of protein kinase (Hayes,
Messenger Ribonucleic Acids for MAC25 and Connective Tissue Growth Factor (CTGF) Are Inversely Regulated during Folliculogenesis and Early Luteogenesis (2000)

Cell proliferation, terminal differentiation, and angiogenesis occur during cycles of follicular and luteal development. In other paradigms, mac25, a potent tumor inhibitor is strongly induced in senescent epithelial cells, whereas CTGF stimulates angiogenesis and wound healing. Using in situ hybridization and immunohistochemistry, we have examined the possibilities that mac25 is inhibited, whereas CTGF is induced during active periods of follicular development and luteogenesis. Ovaries were collected during the follicular and early luteal phases from prostaglandin F2α-treated mature pigs and from slaughterhouse sows. CTGF transcripts were induced during the late preantral stage in granulosa and theca cells concomitantly with the appearance of endothelial cells in the theca. CTGF mRNA expression increased in granulosa cells to a maximum (P < 0.01) in mid-antral follicles but was down regulated (P < 0.01) in preovulatory follicles. In contrast, granulosa cell mac25 mRNA expression was undetectable between the preantral and mid-antral stage but was strongly induced in terminally differentiated granulosa cells of preovulatory follicles. CTGF mRNA and peptide were also detected in the theca externa/interstitium and in vascular endothelial cells of ovarian blood vessels, whereas mac25 transcripts, which were also abundant in ovarian blood vessels increased in the theca interna with follicular development. Transcripts of cyclin D1, a marker of cell proliferation, appeared during the early antral stage and were moderate in granulosa cells but abundant in capillary endothelial cells in the theca interna, underneath the basement membrane. Following ovulation, CTGF and cyclin D1 mRNAs were associated with the migration of endothelial cells into the CL. Subsequently, there was a marked up-regulation of CTGF mRNA expression in granulosa luteins concomitantly with an increase in endothelial cell proliferation within the CL. We hypothesize that CTGF may promote ovarian cell growth and blood vessel formation during follicular and luteal development whereas mac25, a tumor inhibitor, may promote terminal differentiation of granulosa cells in preovulatory follicles.
Phosphorylation of Nuclear Phospholipase C β1 by Extracellular Signal-Regulated Kinase Mediates the Mitogenic Action of Insulin-Like Growth Factor I (2001)

It is well established that a phosphoinositide (PI) cycle which is operationally distinct from the classical plasma membrane PI cycle exists within the nucleus, where it is involved in both cell proliferation and differentiation. However, little is known about the regulation of the nuclear PI cycle. Here, we report that nucleus-localized phospholipase C (PLC) beta1, the key enzyme for the initiation of this cycle, is a physiological target of extracellular signal-regulated kinase (ERK). Stimulation of Swiss 3T3 cells with insulin-like growth factor I (IGF-I) caused rapid nuclear translocation of activated ERK and concurrently induced phosphorylation of nuclear PLC beta1, which was completely blocked by the MEK inhibitor PD 98059. Coimmunoprecipitation detected a specific association between the activated ERK and PLC beta1 within the nucleus. In vitro studies revealed that recombinant PLC beta1 could be efficiently phosphorylated by activated mitogen-activated protein kinase but not by PKA. The ERK phosphorylation site was mapped to serine 982, which lies within a PSSP motif located in the characteristic carboxy-terminal tail of PLC beta1. In cells overexpressing a PLC beta1 mutant in which serine 982 is replaced by glycine (S982G), IGF-I failed to activate the nuclear PI cycle, and its mitogenic effect was also markedly attenuated. Expression of S982G was found to inhibit ERK-mediated phosphorylation of endogenous PLC beta1. This result suggests that ERK-evoked phosphorylation of PLC beta1 at serine 982 plays a critical role in the activation of the nuclear PI cycle and is also crucial to the mitogenic action of IGF-I.
Spontaneous circulation of myeloid-lymphoid–initiating cells and SCID-repopulating cells in sickle cell crisis (2003)

Sickle cell disease (SCD) is an inherited hemoglobinopathy that arises from a single-base substitution at codon 6 of the -globin gene, resulting in the conversion of valine to glutamic acid. It is one of the most common forms of inherited anemia, affecting 150 million people worldwide, predominantly of African or Afro-Caribbean descent.
Reduced infiltration of tumor-associated macrophages in human prostate cancer: association with cancer progression. (2000)

Tumor-associated macrophages (TAMs) are highly active immune effector cells that may either positively or negatively regulate the growth of various malignant cells, depending on the biological context. However, the role of TAMs in human prostate cancer progression is unclear. TAMs were immunohistochemically labeled using a monoclonal (CD68) antibody in radical prostatectomy specimens derived from 81 prostate cancer patients. CD68-positive cells were counted with the aid of a microscope and expressed as macrophage index (MphiI), including TAMs/mm2 total tumor tissue (MphiItotal), TAMs/mm2 tumor stroma (MphiIstroma), and TAMs/mm2 cancer cell area (MphiIcancer). MphiIs were analyzed in association with patients' clinical and pathological stage, recurrence status, and histological grade of the cancer. There were significant inverse relationships between MphiItotal and MphiIstroma and clinical stage (P = 0.016 and P = 0.006, respectively). Reduced MphiItotal was also associated with the presence of positive lymph nodes (P = 0.010). Interestingly, although all of the MphiIs differed between Gleason score groups, only MphiIcancer was positively associated with Gleason score. Univariate analysis of MphiItotal and multivariate analysis of MphiItotal with specific pathological markers revealed that MphiItotal was an independent predictor for disease-free survival after surgery (Cox proportional hazard model, P = 0.044 and P = 0.007, respectively). For patients with high MphiItotal (> or = 185.8, the mean MphiItotal value), the disease-free probability 5 years after surgery was 0.75, which was significantly higher than for those with low MphiItotal (0.31, P = 0.0008). Additional immunohistochemical studies that evaluated cytotoxicity-related biomarkers in stroma-associated mononuclear cells suggested reduced functional activities in highly aggressive prostate cancer compared with less aggressive disease. Our results indicate that reduced MphiItotal is a novel prognostic marker for prostate cancer.
Clinical Predictors of Drug Response in Obsessive-Compulsive Disorder (2001)

The aim of this study was to evaluate which clinical variables might influence the antiobsessional response to proserotonergic drugs in a sample of patients with obsessive-compulsive disorder (OCD). One hundred fifty-nine patients with DSM-IV OCD underwent a 12-week standardized treatment with fluvoxamine, clomipramine, citalopram, or paroxetine. According to treatment response, defined as a reduction of the Yale-Brown Obsessive Compulsive Scale total score >35%, patients were divided into two groups. Ninety patients (56.6%) responded to treatment and 69 (43.4%) did not. Responders had a significantly higher frequency of positive family history for OCD (FH-OCD) in their first-degree relatives, whereas nonresponders had an earlier onset and a higher frequency of "poor insight" subtype and somatic obsessions. The predictive value of all these variables was tested by a stepwise logistic regression analysis that confirmed poor insight and FH-OCD to be the best predictors of poor and good drug treatment response, respectively. These preliminary findings need additional investigations toward a better definition of the genetic and biological heterogeneity of patients with OCD, and they underlie the importance of collecting the insight score and family history for psychiatric disorders in the pretreatment assessment.
Degradation of basement membrane type IV collagen and lung subendothelial matrix by rat mammary adenocarcinoma cell clones of differing metastatic potentials. (1987)

A series of rat 13762NF mammary adenocarcinoma cell clones and subclones of various lung metastatic potentials were examined for their abilities to degrade rat lung subendothelial matrix and purified basement membrane type IV collagen. Metastatic potentials were simultaneously determined based on the ability to form "spontaneous" lung metastases after s.c. injection or "experimental" lung metastases after i.v. injection of cells. Microvessel endothelial cells isolated from rat lung were grown in vitro, and the subendothelial matrix containing type IV collagen was metabolically labeled with [3H]proline. When mammary adenocarcinoma cells were placed on the isolated subendothelial matrix, fragmentation and solubilization of [3H]proline-labeled components were observed; highly metastatic 13762NF cells solubilized the matrix at higher rates than did poorly metastatic cells. The 13762NF cells were assayed for type IV collagenolytic activity using [3H]proline-labeled type IV collagen purified from Engelbreth-Holm-Swarm tumor as a substrate. We found excellent correlation between the type IV collagenolytic activities of living cells and their "spontaneous" lung metastatic potentials (r = 0.993). The levels of type IV collagenolytic activity in the conditioned medium depended on the cell culture conditions. In the presence or absence of acid-treated fetal bovine serum, highly metastatic cells secreted higher amounts of type IV collagenolytic enzymes in active and latent forms than did poorly metastatic cells. Incubation of procollagen type IV with medium conditioned by highly metastatic 13762NF cells and treated with trypsin resulted in the production of several large fragments characteristic of type IV collagen. The results suggest that enzymatic degradation of basement membrane type IV collagen is important in lung metastasis of 13762NF mammary adenocarcinoma cells.
Prospects for treatment of human retrovirus-associated diseases. (1985)

Overwhelming evidence has been obtained over the past 2 years that human T-cell leukemia virus type III (HTLV-III) is the primary cause of acquired immunodeficiency syndrome. The direct cytopathic effect of the virus on T4 helper cells demonstrated in vitro is probably responsible for the depletion of this critical population of cells in affected individuals which results in a series of devastating immunological abnormalities. It follows that any approaches effective in suppressing the virulent virus would be of benefit to the infected patient. The vast amount of knowledge about retroviruses in general, and the rapidly accumulating information about HTLV-III in particular, makes it likely that a targeted approach for development of antiviral agents will bear fruit. General strategies further making use of chemical and biological agents as well as genetic manipulations are discussed.
Volumetric microvascular imaging of human retina using optical coherence tomography with a novel motion contrast technique (2009)

Phase variance-based motion contrast imaging is demonstrated using a spectral domain optical coherence tomography system for the in vivo human retina. This contrast technique spatially identifies locations of motion within the retina primarily associated with vasculature. Histogram-based noise analysis of the motion contrast images was used to reduce the motion noise created by transverse eye motion. En face summation images created from the 3D motion contrast data are presented with segmentation of selected retinal layers to provide non-invasive vascular visualization comparable to currently used invasive angiographic imaging. This motion contrast technique has demonstrated the ability to visualize resolution-limited vasculature independent of vessel orientation and flow velocity.
Translational regulation of GluR2 mRNAs in rat hippocampus by alternative 3′ untranslated regions (2009)

The glutamate receptor 2 (GluR2) subunit determines many of the functional properties of the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate subtype of glutamate receptor. The roles of untranslated regions (UTRs) in mRNA stability, transport, or translation are increasingly recognized. The 3' end of the GluR2 transcripts are alternatively processed to form a short and long 3'UTR, giving rise to two pools of GluR2 mRNA of 4 and 6 kb in length, respectively, in the mammalian brain. However, the role of these alternative 3'UTRs in GluR2 expression has not been reported. We demonstrate that in the cytoplasm of rat hippocampus, native GluR2 mRNAs bearing the long 3'UTR are mostly retained in translationally dormant complexes of ribosome-free messenger ribonucleoprotein (mRNP), whereas GluR2 transcripts bearing the short 3'UTR are predominantly associated with actively translating ribosomes. One day after pilocarpine-induced status epilepticus (SE), the levels of both long and short GluR2 transcripts were markedly decreased in rat hippocampus. However, GluR2 mRNAs bearing the long 3'-UTRs were shifted from untranslating mRNP complexes to ribosome-containing complexes after SE, pointing to a selective translational derepression of GluR2 mRNA mediated by the long 3'UTR. In Xenopus oocytes, expression of firefly luciferase reporters bearing alternative GluR2 3'UTRs confirmed that the long 3'UTR is sufficient to suppress translation. The stability of reporter mRNAs in oocytes was not significantly influenced by alternative 5' or 3'UTRs of GluR2 over the time period examined. Overall, our findings that the long 3'UTR of GluR2 mRNA alone is sufficient to suppress translation, and the evidence for seizure-induced derepression of translation of GluR2 via the long 3'UTR strongly suggests that a regulatory signaling mechanism exists that differentially targets GluR2 transcripts with alternative 3'UTRs.
Determination of residues involved in ligand binding and signal transmission in the human IFN-alpha receptor 2. (1999)

The human IFN-alpha receptor (hIFNAR) is a complex composed of at least two chains, hIFNAR1 and hIFNAR2. We have performed a structure-function analysis of hIFNAR2 extracellular domain regions using anti-hIFNAR2 mAbs (1D3, 1F3, and 3B7) and several type I human IFNs. These mAbs block receptor activation, as determined by IFN-stimulated gene factor 3 formation, and block the antiviral cytopathic effects induced by type I IFNs. We generated alanine substitution mutants of hIFNAR2-IgG and determined that regions of hIFNAR2 are important for the binding of these blocking mAbs and hIFN-alpha2/alpha1. We further demonstrated that residues E78, W101, I104, and D105 are crucial for the binding of hIFN-alpha2/alpha1 and form a defined protrusion when these residues are mapped upon a structural model of hIFNAR2. To confirm that residues important for ligand binding are indeed important for IFN signal transduction, we determined the ability of mouse L929 cells expressing hIFNAR2 extracellular domain mutants to mediate hIFN signal. hIFN-alpha8, previously shown to signal a response in L929 cells expressing hIFNAR1, was unable to signal in L929 cells expressing hIFNAR2. Transfected cells expressing hIFNAR2 containing mutations at residues E78, W101, I104, or D105 were unresponsive to hIFN-alpha2, but remained responsive to hIFN-beta. In summary, we have identified specific residues of hIFNAR2 important for the binding to hIFN-alpha2/1 and demonstrate that specific regions of the IFNAR interact with the subspecies of type I IFN in different manners.
Pelvic organs in premenarcheal girls: real-time ultrasonography. (1984)

Age-related changes in uterine and ovarian morphology and size were studied in 114 normal premenarcheal girls using a real-time mechanical sector scanner. Reference growth values were obtained for total uterine length, anteroposterior diameters of the corpus and cervix, corpus/cervix ratio, and uterine and ovarian volumes. Up to 7 years of age uterine size was not influenced by age and there was a relative predominance of the cervix over the corpus. Thereafter the uterus underwent a regular increase in size and the corpus gradually became larger than the cervix. Ovarian volume was relatively stable up to 5 years, when regular age-related growth started, associated with an increase in cystic functional changes in the ovary. As uterine and ovarian morphology and size are reliable indicators of the degree of sex-hormone stimulation, real-time ultrasound offers a rapid method of studying normal and abnormal pubertal development in girls.
Abstract 820: Molecular markers for head and neck cancer detection (2010)

Abstract Introduction: Fifty thousand new cases of HNSCC are diagnosed in the United States each year. Unfortunately, most of these cases are advanced and only cured about 40% of the time. Cure rates could reach over 80% if diagnosed in earlier stages. We are developing a simple and inexpensive molecular screening test for the early detection of HNSCC. The markers under investigation are detectable in oral rinses and include soluble CD44 (solCD44), hyaluronic acid (HA) and total protein. Materials and Methods: To study the population most likely to benefit from this early detection test, high-risk controls were identified by their smoking and/or drinking behavior from primary care clinics. They received a complete head and neck exam and had no clinical evidence of malignancy or premalignancy. Low-risk controls were normal volunteers. All subjects completed a detailed questionnaire including demographic, socioeconomic, risk factor and general health information. Oral samples were collected using a previously described swish and gargle method. We performed the solCD44, HA and protein assays in blinded fashion on oral rinses from 18 HNSCC cases, 18 frequency-matched high-risk controls and 21 low-risk controls using previously reported ELISA and ELISA-like assays. Results: We statistically assessed the adequacy of matching between the cases and high-risk controls with respect to age, gender, race, socioeconomic status, tobacco and alcohol exposure and oral health. There were no significant differences between cases and controls for any of these variables except for a borderline significant difference in race. Log2solCD44 levels were significantly higher in cancer cases (2.42 ng/ml) and high-risk controls (2.12 ng/ml) compared to low risk controls (0.64 ng/ml, p&amp;lt;0.05). Log2protein levels were also higher in cancer cases (0.88 mg/ml) and high-risk controls (0.97 mg/ml) compared to low-risk controls (0.52, p&amp;lt;0.05). Following receiver operating curve analysis, the AUC for distinguishing high-risk controls from low-risk controls was 0.94 for solCD44 and 0.82 for protein. The AUC for distinguishing cancer from low-risk controls was 0.95 for solCD44 and 0.77 for protein. After adjusting for race, the AUC for distinguishing cancer from high-risk controls was 0.76 for solCD44 and 0.68 for protein. Both of these were better for the nonwhite group (0.84 for solCD44 and 0.83 for protein). Conclusions: In this preliminary data set, the solCD44 and protein test appear to effectively distinguish HNSCC cases from high and low-risk controls. Race may have an impact on results. Further work including more subjects with longer follow-up must be done to confirm or refute these findings. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 820.
ChemInform Abstract: Building Blocks for Oligonucleotide Analogues with Dimethylene Sulfide, Sulfoxide, and Sulfone Group Replacing Phosphodiester Linkages. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
NADPH Oxidase, NOX1, Mediates Vascular Injury in Ischemic Retinopathy (2013)

Our findings suggest that strategies targeting NOX1 have the potential to be effective treatments for a range of ischemic retinopathies.