gebhart/patrepeval huggingface dataset:
Block copolymers and conventional lithography (2006)

The lithographic process is arguably the key enabling technology for the digital age. Hundreds of millions of devices can be fabricated on a single chip because patterns with features as small as 50 nm can be written with a remarkable level of perfection, in registration with the underlying substrate, and with complex geometries. As the drive to pattern at ever shrinking length scales continues, however, new imaging materials may be required to meet manufacturing constraints. We highlight some of the recent advances in integrating self-assembling block copolymers into the conventional lithographic process to address issues of resolution and process control.
Autism‐associated familial microdeletion of Xp11.22 (2008)

We describe two brothers with autistic disorder, intellectual disability (ID) and cleft lip/palate with a microdeletion of Xp11.22 detected through screening individuals with autism spectrum disorders (ASDs) for microdeletions and duplications using 1-Mb resolution array comparative genomic hybridization. The deletion was confirmed by fluorescence in situ hybridization/real-time quantitative polymerase chain reaction (RT-qPCR) and shown to be inherited from their unaffected mother who had skewed (100%) X inactivation of the aberrant chromosome. RT-qPCR characterization of the del(X)(p11.22) region ( approximately 53,887,000-54,359,000 bp) revealed complete deletion of the plant homeodomain finger protein 8 (PHF8) gene as well as deletions of the FAM120C and WNK lysine-deficient protein kinase 3 (WNK3) genes, for which a definitive phenotype has not been previously characterized. Xp11.2 is a gene-rich region within the critical linkage interval for several neurodevelopmental disorders. Rare interstitial microdeletions of Xp11.22 have been recognized with ID, craniofacial dysmorphism and/or cleft lip/palate and truncating mutations of the PHF8 gene within this region. Despite evidence implicating genes within Xp11.22 with language and cognitive development that could contribute to an ASD phenotype, their involvement with autism has not been systematically evaluated. Population screening of 481 (319 males/81 females) and 282 X chromosomes (90 males/96 females) in respective ASD and control cohorts did not identify additional subjects carrying this deletion. Our findings show that in addition to point mutations, a complete deletion of the PHF8 gene is associated with the X-linked mental retardation Siderius-Hamel syndrome (OMIM 300263) and further suggest that the larger size of the Xp11.22 deletion including genes FAM120C and WNK3 may be involved in the pathogenesis of autism.
The many faces of epidermal growth factor repeats. (1990)

Epidermal growth factor (EGF) is a short peptide with a distinctive motif of six cysteines. This motif is found in many different proteins of diverse functions. One approach to determining the functional utility of EGF repeats is to undertake a methodical analysis of each individual protein. While this approach has met with some success, it has been applied to only a small fraction of all the EGF repeat-bearing proteins. A second approach is to consider all these proteins as a whole but give particular attention to structural and functional similarities. This review attempts a broad, although not comprehensive, survey of the families of proteins containing EGF repeats, with particular emphasis on the relative distribution of calcium-binding and noncalcium-binding EGF repeats.
HIV binding, penetration, and primary infection in human cervicovaginal tissue (2005)

We have developed human cervicovaginal organ culture systems to examine the initiating events in HIV transmission after exposure to various sources of HIV infectivity, including semen. Newly infected cells were detected in the cervical submucosa 3-4 days after exposure to a primary HIV isolate. At earlier times, extensive and stable binding occurred when cervical surfaces were exposed to virions or seminal cells. Cervical mucus provided some protection for the endocervical surface, by physically trapping virions and seminal cells. Confocal microscopy combined with 3D surface reconstruction revealed that virions could both bind to the external surface of the cervical epithelium and actually penetrate beneath the epithelial surface. In quantitative assays, pretreatment with a blocking antibody directed against beta1 integrin reduced HIV virion binding. Collectively, these results highlight a continuum of complex interactions that occurs when natural sources of HIV infectivity are deposited onto mucosal surfaces in the female reproductive tract.
Adrenomedullin (2005)

Adrenomedullin (AM) is a vasodilator peptide having a wide range of biological actions such as reduction of oxidative stress and inhibition of endothelial cell apoptosis. The AM gene is expressed in vascular walls, and AM was found to be secreted from cultured vascular endothelial cells, smooth muscle cells, and adventitial fibroblasts. Plasma AM levels in patients with arteriosclerotic vascular diseases are elevated in possible association with the severity of the disease. When administered over a relatively short period, AM dilates blood vessels via an endothelium-dependent or independent mechanism. Experiments in vitro have shown that AM exerts multiple actions on cultured vascular cells, which are mostly protective or inhibitory against vascular damage and progression of arteriosclerosis. Either prolonged infusion or overexpression of AM suppressed intimal thickening, fatty streak formation, and perivascular hyperplasia in rodent models for vascular remodeling or atherosclerosis. Intimal thickening induced by periarterial cuff was more severe in AM gene-knockout mice than their littermates, suggesting a protective role for endogenous AM. Moreover, AM has recently been suggested to possess angiogenetic properties. Collectively, a body of evidence suggests that AM participates in the mechanism against progression of vascular damage and remodeling, thereby alleviating the ischemia of tissues and organs.
The Veneration of Military rule Versus the Rule of Law (1994)

Individuals of lower socioeconomic status presented at more advanced stage of the disease when developing neovascular age-related macular degeneration in the first eye but not in the second eye. The research underscores the importance of improving referral patterns and awareness for the lowest socioeconomic status classes.
“Sentinel” Circulating Tumor Cells Allow Early Diagnosis of Lung Cancer in Patients with Chronic Obstructive Pulmonary Disease (2014)

Chronic obstructive pulmonary disease (COPD) is a risk factor for lung cancer. Migration of circulating tumor cells (CTCs) into the blood stream is an early event that occurs during carcinogenesis. We aimed to examine the presence of CTCs in complement to CT-scan in COPD patients without clinically detectable lung cancer as a first step to identify a new marker for early lung cancer diagnosis. The presence of CTCs was examined by an ISET filtration-enrichment technique, for 245 subjects without cancer, including 168 (68.6%) COPD patients, and 77 subjects without COPD (31.4%), including 42 control smokers and 35 non-smoking healthy individuals. CTCs were identified by cytomorphological analysis and characterized by studying their expression of epithelial and mesenchymal markers. COPD patients were monitored annually by low-dose spiral CT. CTCs were detected in 3% of COPD patients (5 out of 168 patients). The annual surveillance of the CTC-positive COPD patients by CT-scan screening detected lung nodules 1 to 4 years after CTC detection, leading to prompt surgical resection and histopathological diagnosis of early-stage lung cancer. Follow-up of the 5 patients by CT-scan and ISET 12 month after surgery showed no tumor recurrence. CTCs detected in COPD patients had a heterogeneous expression of epithelial and mesenchymal markers, which was similar to the corresponding lung tumor phenotype. No CTCs were detected in control smoking and non-smoking healthy individuals. CTCs can be detected in patients with COPD without clinically detectable lung cancer. Monitoring "sentinel" CTC-positive COPD patients may allow early diagnosis of lung cancer.
Vitamin B 6 Is Required for Full Motility and Virulence in Helicobacter pylori (2010)

Despite recent advances in our understanding of how Helicobacter pylori causes disease, the factors that allow this pathogen to persist in the stomach have not yet been fully characterized. To identify new virulence factors in H. pylori, we generated low-infectivity variants of a mouse-colonizing H. pylori strain using the classical technique of in vitro attenuation. The resulting variants and their highly infectious progenitor bacteria were then analyzed by global gene expression profiling. The gene expression levels of five open reading frames (ORFs) were significantly reduced in low-infectivity variants, with the most significant changes observed for ORFs HP1583 and HP1582. These ORFs were annotated as encoding homologs of the Escherichia coli vitamin B(6) biosynthesis enzymes PdxA and PdxJ. Functional complementation studies with E. coli confirmed H. pylori PdxA and PdxJ to be bona fide homologs of vitamin B(6) biosynthesis enzymes. Importantly, H. pylori PdxA was required for optimal growth in vitro and was shown to be essential for chronic colonization in mice. In addition to having a well-known metabolic role, vitamin B(6) is necessary for the synthesis of glycosylated flagella and for flagellum-based motility in H. pylori. Thus, for the first time, we identify vitamin B(6) biosynthesis enzymes as novel virulence factors in bacteria. Interestingly, pdxA and pdxJ orthologs are present in a number of human pathogens, but not in mammalian cells. We therefore propose that PdxA/J enzymes may represent ideal candidates for therapeutic targets against bacterial pathogens.
La Princesa de la intrigas (2012)

Con una amplia perspectiva, Angeles Caso sopesa las maquinaciones y genialidades de Mariana de La Tremoille, princesa de los Ursinos, durante anos la mujer mas influyente en la corte de Felipe V.
Release of tumor necrosis factor by alveolar macrophages of patients with sarcoidosis. (1990)

Tumor necrosis factor (TNF) is a monokine released by macrophages and is important in the inflammatory response. We compared the spontaneous release of TNF by alveolar macrophages (AMs) from patients with symptomatic pulmonary sarcoidosis, some of whom were receiving corticosteroid therapy, with AMs from control smokers. TNF was released from AMs of sarcoidosis patients at significantly higher levels than was released by control AM subjects (sarcoids, 15 U/ml [0 to 1140 U (median [range]]); controls, all less than 5 U/ml, p less than 0.01). By using a specific polyclonal antibody, the detected TNF was found to be TNF-alpha. Among the sarcoidosis patients, the amount of TNF released was significantly lower for those patients given treatment with corticosteroids (5 U/ml [0 to 15 U/ml]) compared with untreated persons (50 U/ml [0 to 1140 U/ml], p less than 0.05). In vitro studies demonstrated that incubation of peripheral blood monocytes or AMs with dexamethasone for 42 hours suppressed subsequent release of TNF. We conclude that AMs from sarcoidosis patients often spontaneously release TNF and this release is suppressed by prolonged corticosteroid therapy.
The PLA2G6 gene in early‐onset Parkinson's disease (2011)

Future studies should investigate the prevalence of these SNPs in other PD populations and larger control groups and also address possible genetic alterations in the remaining parts of the PLA2G6 gene.
Oral idarubicin, dexamethasone and vincristine (VID) in the treatment of multiple myeloma. (1997)

In order to replace the central venous line necessary for continuous infusion of vincristine and doxorubicin with high-dose dexamethasone (VAD) and to avoid hospitalization, we evaluated the efficacy and toxicity of oral idarubicin, vincristine and dexamethasone (VID) in patients with multiple myeloma. Vincristine (1.6 mg/m2, max 2 mg) was given as a bolus injection on day 1. Idarubicin was given in capsules 10 mg/m2/day for days 1-4 with an intraindividual dose escalation, 40 mg dexamethasone were given on days 1-4, 9-12, 17-20. Treatment cycles were repeated every 28 days. At this interim analysis, 53 patients have been entered into the ongoing trial; 46 patients are evaluable for toxicity. The median age was 60 years (interquartile range, 52-65). 46% were primary or secondary refractory, 20% had previously been treated with VAD and 30% had previously untreated disease, 4% had two or more relapses. Four patients died within 2 months from entry and were considered as early deaths (8.7%). 45% of the 42 patients evaluable for efficacy achieved a partial remission and 26% a minor remission. The median reduction of the M-component was 43% (interquartile range, 25-64%). VID is an effective and convenient alternative to VAD even in relapsed or refractory patients.
NKT Cell Activation Mediates Neutrophil IFN-γ Production and Renal Ischemia-Reperfusion Injury (2007)

Previous work has shown that ischemia-reperfusion (IR) injury (IRI) is dependent on CD4(+) T cells from naive mice acting within 24 h. We hypothesize that NKT cells are key participants in the early innate response in IRI. Kidneys from C57BL/6 mice were subjected to IRI (0.5, 1, 3, and 24 h of reperfusion). After 30 min of reperfusion, we observed a significant increase in CD4(+) cells (145% of control) from single-cell kidney suspensions as measured by flow cytometry. A significant fraction of CD4(+) T cells expressed the activation marker, CD69(+), and adhesion molecule, LFA-1(high). Three hours after reperfusion, kidney IFN-gamma-producing cells were comprised largely of GR-1(+)CD11b(+) neutrophils, but also contained CD1d-restricted NKT cells. Kidney IRI in mice administered Abs to block CD1d, or deplete NKT cells or in mice deficient of NKT cells (Jalpha18(-/-)), was markedly attenuated. These effects were associated with a significant decrease in renal infiltration and, in activation of NKT cells, and a decrease in IFN-gamma-producing neutrophils. The results support the essential role of NKT cells and neutrophils in the innate immune response of renal IRI by mediating neutrophil infiltration and production of IFN-gamma.
Recognition of human gastrointestinal cancer neoantigens by circulating PD-1+ lymphocytes (2019)

Tumor-resident lymphocytes can mount a response against neoantigens expressed in microsatellite-stable gastrointestinal (GI) cancers, and adoptive transfer of neoantigen-specific lymphocytes has demonstrated antitumor activity in selected patients. However, whether peripheral blood could be used as an alternative minimally invasive source to identify lymphocytes targeting neoantigens in patients with GI cancer with relatively low mutation burden is unclear. We used a personalized high-throughput screening strategy to investigate whether PD-1 expression in peripheral blood could be used to identify CD8+ or CD4+ lymphocytes recognizing neoantigens identified by whole-exome sequencing in 7 patients with GI cancer. We found that neoantigen-specific lymphocytes were preferentially enriched in the CD8+PD-1+/hi or CD4+PD-1+/hi subsets, but not in the corresponding bulk or PD-1- fractions. In 6 of 7 individuals analyzed we identified circulating CD8+ and CD4+ lymphocytes targeting 6 and 4 neoantigens, respectively. Moreover, neoantigen-reactive T cells and a T cell receptor (TCR) isolated from the CD8+PD-1+ subsets recognized autologous tumor, albeit at reduced levels, in 2 patients with available cell lines. These data demonstrate the existence of circulating T cells targeting neoantigens in GI cancer patients and provide an approach to generate enriched populations of personalized neoantigen-specific lymphocytes and isolate TCRs that could be exploited therapeutically to treat cancer.
ChemInform Abstract: Importance of Metal‐Oxide Support Wetting and Interactions on Understanding of Physical and Chemical Behaviors of Supported Metal Catalysts (1995)

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.
Characteristics of an RNA Diels−Alderase Active Site (1999)

The active site components and substrate specificity of an RNA Diels−Alderase (DA22) were investigated. Diels−Alderase activity was found to be highly dependent on a unique 5-position pyridyl modified uridine. Even closely related pyridyl modifications failed to yield active catalysts. Substrate specificity of this Diels−Alderase was remarkable. Experiments with alternative diene and dienophile substrates showed the active site of the Diels−Alderase to be highly discriminating, even against molecules of similar reactivity and structure. Inhibition studies with a series of product analogues established that the RNA recognizes functional components in and around the reaction center of both the diene and the dienophile. Taken together, these results suggest that DA22 can fold into a structure that produces an intricate metal/ligand dependent active site capable of highly specific molecular recognition.
Phase aberration correction in medical ultrasound using speckle brightness as a quality factor (1989)

Medical ultrasonic images are degraded by tissues with inhomogeneous acoustic velocities. The resulting phase aberration raises the off-peak response of the imaging system's point spread function (PSF), decreasing dynamic range. In extreme cases, multiple images of a single target are displayed. Phase aberration may become a limiting factor to image quality as ultrasonic frequency and aperture size are increased in order to improve spatial resolution. A method is proposed to correct for unknown phase aberration, which uses speckle brightness as a quality factor. The phase delays of a phased array transducer are modified, element by element, to maximize mean speckle brightness in a region of interest. The technique proposed is analogous to the correction technique used by Muller and Buffington [J. Opt. Soc. Am. 64 (9), 1200-1209 (1974)] to adaptively focus incoherent optical telescopes. The method is demonstrated using a computer model with several different simulated aberration profiles. With this model, mean speckle brightness is calculated using the two-dimensional PSF. Experiments have also been conducted in which speckle brightness is shown to increase as the phase delays of an ultrasonic scanner are modified in order to compensate for a rippled aberrating layer made of silicone rubber. The characteristics of the proposed method, and the possibility of employing it clinically to correct for unknown inhomogeneities in acoustic velocity, are discussed.
Detection of tumorigenesis in urinary bladder with optical coherence tomography: optical characterization of morphological changes (2002)

Most transitional cell tumorigenesis involves three stages of subcellular morphological changes: hyperplasia, dysplasia and neoplasia. Previous studies demonstrated that owing to its high spatial resolution and intermediate penetration depth, current OCT technology including endoscopic OCT could delineate the urothelium, submucosa and the upper muscular layers of the bladder wall. In this paper, we will discuss the sensitivity and limitations of OCT in diagnosing and staging bladder cancer. Based on histomorphometric evaluations of nuclear morphology, we modeled the resultant backscattering changes and the characteristic changes in OCT image contrast. In the theoretical modeling, we assumed that nuclei were the primary sources of scattering and were uniformly distributed in the uroepithelium, and compared with the results of the corresponding prior OCT measurements. According to our theoretical modeling, normal bladder shows a thin, uniform and low scattering urothelium, so does an inflammatory lesion except thickening in the submucosa. Compared with a normal bladder, a hyperplastic lesion exhibits a thickened, low scattering urothelium whereas a neoplastic lesion shows a thickened urothelium with increased backscattering. These results support our previous animal study that OCT has the potential to differentiate inflammation, hyperplasia, and neoplasia by quantifying the changes in urothelial thickening and backscattering. The results also suggest that OCT might not have the sensitivity to differentiate the subtle morphological changes between hyperplasia and dysplasia based on minor backscattering differences.
Molecular Imaging: Looking at Problems, Seeing Solutions (2003)

Noninvasive molecular-imaging technologies are providing researchers with exciting new opportunities to study small-animal models of human disease. With continued improvements in instrumentation, identification of better imaging targets by genome-based approaches, and design of better imaging probes by innovative chemistry, these technologies promise to play increasingly important roles in disease diagnosis and therapy.
Carotenoid Pigmentation Affects the Volatile Composition of Tomato and Watermelon Fruits, As Revealed by Comparative Genetic Analyses (2005)

Tomato near-isogenic lines differing in fruit carotenogenesis genes accumulated different aroma volatiles, in a strikingly similar fashion as compared to watermelon cultivars differing in fruit color. The major volatile norisoprenoids present in lycopene-containing tomatoes and watermelons were noncyclic, such as geranial, neral, 6-methyl-5-hepten-2-one, 2,6-dimethylhept-5-1-al, 2,3-epoxygeranial, (E,E)-pseudoionone, geranyl acetone, and farnesyl acetone, seemingly derived from lycopene and other noncyclic tetraterpenoids. Beta-ionone, dihydroactinodiolide, and beta-cyclocitral were prominent in both tomato and watermelon fruits containing beta-carotene. Alpha-ionone was detected only in an orange-fleshed tomato mutant that accumulates delta-carotene. A yellow flesh (r) mutant tomato bearing a nonfunctional psy1 gene and the yellow-fleshed watermelon Early Moonbeam, almost devoid of carotenoid fruit pigments, also lacked norisoprenoid derivatives and geranial. This study provides evidence, based on comparative genetics, that carotenoid pigmentation patterns have profound effects on the norisoprene and monoterpene aroma volatile compositions of tomato and watermelon and that in these fruits geranial (trans-citral) is apparently derived from lycopene in vivo.
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis (1997)

After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.
Symptoms, Cognitive Functioning, and Adaptive Skills in Geriatric Patients With Lifelong Schizophrenia: A Comparison Across Treatment Sites (1998)

Cognitive impairment is a predictor of both overall outcome and specific adaptive deficits. These data suggest that interventions aimed at cognitive impairment may have an impact on overall functional status. In comparison, positive symptom severity is less strongly correlated with overall adaptive outcome and is uncorrelated with specific deficits in adaptive skills.