gebhart/patrepeval huggingface dataset:
CD31/PECAM Automated and Quantitative Immunocytochemical Assays in Breast Carcinomas:<i>Correlation With Patient Follow-up</i> (1997)

The purpose of this study was to determine the prognostic significance of quantitative CD31 immunohistochemical assays. CD31 assays were performed on a series of 167 breast carcinoma specimens under optimal technical conditions that involved frozen sections, an automated immunoperoxidase technique, and computer-assisted analysis of digitized colored microscopic images. Results of automated quantitative immunohistochemical assays were correlated with patient follow-up (9.6 years). Patients were divided into two subgroups: those who had axillary lymph node-positive (N+) disease and those who had lymph node-negative (N-) disease. The marked immunocytochemical expression of CD31 in tumors (cutoff point, 20%) was significantly (P = .033) associated with a poor overall survival rate (Kaplan-Meier, log rank test); however, a significant association was not observed in the N+ and N- subgroups. CD31-immunostained tumor cell surfaces larger than 20% correlated with the metastasis-free survival rate (P = .004) in all patients and in the N+ subgroup (P = .005) but not in the N- subgroup. In addition, marked immunocytochemical expression of CD31 correlated with the short-term disease-free survival rate (P = .04) in the N+ subgroup but not in the N- subgroup. In multivariate analysis (proportional hazards regression, Cox model) the prognostic significance of CD31 was independent of tumor size and histologic type but not of grade. The results suggest that, under optimal technical conditions (automated and quantitative immunohistochemical assays on frozen sections), immunohistochemical expression of CD31 is a significant prognostic indicator of overall and metastasis-free survival rates. CD31 has limited prognostic value, however, and is not a completely independent prognostic indicator because it is related to nodal status.
Preference for Geometric Patterns Early in Life as a Risk Factor for Autism (2010)

A preference for geometric patterns early in life may be a novel and easily detectable early signature of infants and toddlers at risk for autism.
Influence of Osteogenic Protein-1 (OP-l;BMP-7) and Transforming Growth Factor-βl on Bone Formation<i>In Vitro</i> (1996)

The bone morphogenetic proteins (BMPs) and transforming growth factor-beta s (TGF-beta s), are a group of structurally related proteins which have been shown to stimulate bone formation in vivo. Since these proteins are concentrated in the organic matrix of bone and would be released during bone resorption, they are likely to have a profound effect on the remodeling bone and may provide a link between bone resorption and bone formation. We are using primary cultures of fetal rat calvarial cells (FRCC) to study the independent and combined effects of OP-1/BMP-7 and TGF-beta 1 on bone cells at different stages of differentiation in order to identify responding cell populations and target genes. We have confirmed prior reports that OP-1 stimulates, while TGF-beta 1 inhibits, osteogenic differentiation in this system. The increase in both number and size of the mineralized nodules induced by OP-1 was accompanied by increased expression of alkaline phosphatase and type I collagen with an induction of bone sialoprotein (BSP) suggesting that OP-1 stimulates both differentiation and clonal expansion of osteoblastic cells. Interestingly, TGF-beta 1 abrogated OP-1 induced nodule formation. Despite these opposing effects on osteogenic differentiation, TGF-beta 1 (Wrana et al, 1991) and OP-1 both stimulated a rapid induction of osteopontin (OPN) mRNA in confluent FRCC cultures enriched in pre-osteoblastic cells. In contrast, when OP-1 was added to nodule-forming cultures which are enriched in osteoblastic cells, there was only a weak induction of OPN. Moreover, while the expression of one marker for mature osteoblasts (BSP) was refractory to OP-1, another (osteocalcin) was markedly stimulated. Thus OP-1 has selective effects on bone matrix protein expression that are dependent on the differentiated state of the cells.
Analysis of 3D Dynamic Urban Scenes Based on LiDAR Point Cloud Sequences (2013)

In recent years, the spread of domestic, industrial and research robots and the robotic vehicles made 3D sensory information (such as LiDAR sensors) more and more widespread opposed to the conventional 2D image sensory information.A modern LiDAR sensor on board of a vehicle provides enough data to make us able to interpret the space surrounding the vehicle even at large scenes containing a whole street segment.In this paper, we present a method to reconstruct.The input of this procedure is a LiDAR sensor mounted on a car, which outputs a data stream covering more than 100 meters radius of space, collecting data at 15 Hz.The recording is in real environment on the streets of Budapest in real time, while the processing is offline, implemented on CPU keeping in mind the future implementation on GPUs to reach real time data processing.The data is provided by a Velodyne HDL-64E high performance LiDAR device.The aim is to segment several region classes (such as roads, building walls, vegetation) and to identify specified objects (such as people, vehicles, traffic signs) in the point clouds through a presegmentation step.To achieve this classification, we need several features such as the color and geometrical properties of the specified objects and their possible geometrical and physical interactions.Also, we need to take into account the time domain features calculated based on the LiDAR data stream.After this presegmentation step we are able to reconstruct building facades in 3D and to track the detected objects in the 3D space.Also, in the future, this processed data set can be registered against 2D images provided by conventional cameras to reproduce realistic, colored 3D virtual spaces.
The Proton-Translocating ATPase of Escherichia Coli (1990)

The purpose of this review is to provide an up-to-date summary of E. coli proton-translocating F1F0ATPase. From work on this enzyme, new insights have been gained in the areas of bacterial physiology and energy metabolism, mechanism of enzyme action, mechanism of ion transport through membranes, structure of membrane proteins, mechanism of energy coupling, and regulation of complex enzyme expression and assembly. An important and pressing need is for more structural information. High-resolution structural analyses of F1F0 have not progressed far, and this is likely to present a road block unless overcome. One possibility is to crystallize or apply nuclear magnetic resonance spectroscopy to isolated subunits available in native form from E. coli F1F0. In this way, one might incrementally build a structure of the F1F0 complex. Static views, however, are unlikely to provide a complete picture of a dynamic enzyme such as this, in which long-range interactions between F0 and F1 and cooperative interactions between nucleotide-binding sites play such an important role in catalysis. Mutagenesis and reversion analysis are two powerful techniques, which, combined with direct enzymological measurements, can be exploited in the immediate future to study the intriguing dynamic aspects of F1F0 function. Many questions remain to challenge us. Regulation of enzyme activity in the cell is not understood. The role of the noncatalytic nucleotide sites is unknown. The assembly pathway and regulation of expression are not established. The mechanisms of H+ translocation and catalysis seem to be proving amenable to analysis, and further advances in these areas can be expected. Long-range conformational interaction between the H+ conduction machinery in F0 and the catalytic sites in F1 seems basic to energy coupling; a major future goal is to provide a realistic physical explanation to validate this concept.
Assessment of in Vitro Applicability of Reversibly Immortalized NKNT-3 Cells and Clonal Derivatives (2006)

In vitro applications of human hepatocytes, such as bioartificial livers and toxicity assays, require thoroughly testing of human cell lines prior to using them as alternative cell sources. The reversibly immortalized NKNT-3 cell line was reported to show clear in vivo functionality. Here, NKNT-3 cells were tested for their in vitro applicability. Low-passage (P2) and high-passage (P28) NKNT-3 cells and clonal derivatives were characterized for reversion of immortalization, heterogeneity, and hepatic functionality. Reversion with reduced expression of immortalizing agent could be established. However, during culturing the cells lost the capacity to be selected for completed reversion. The phenotypic instability is probably associated with heterogeneity in the culture, as clonal derivatives of P2 cells varied in morphology, growth, and reversion characteristics. The mRNA levels of genes related with hepatic differentiation increased 4-20-fold after reversion. However, the levels never exceeded 0.1% of that detected in liver and no urea production nor ammonia elimination was detected. Additionally, activities of different cytochrome P450s were limited. In conclusion, the NKNT-3 culture is heterogeneous and unstable and the in vitro functionality is relatively low. These findings emphasize that in vivo testing of hepatic cell lines is little informative for predicting their value for in vitro applications.
Arbeitsgemeinschaft Minimalinvasive Mammainterventionen (AG MiMi): Ziele – Struktur – erste Arbeiten (2004)

Die Palette der minimal invasiven Techniken im Bereich Mammadiagnostik und Therapie wird kontinuierlich größer. Dem Anwender stellen sich dadurch Fragen bezüglich Indikation, Komplikationsrate, Kosten etc. Im Juli 2003 wurde AG MiMi unter dem Dach der Deutschen Gesellschaft für Senologie gegründet. Ziele dieser Arbeitsgruppe sind u.a.: wissenschaftliche Aufarbeitung der einzelnen Techniken, beratende Funktion bei Konsensusempfehlungen, Durchführung von Fortbildungsveranstaltungen, zentrales Biopsieregister, Literatursammlung, interaktive Internetpräsentation. Die erste wissenschaftliche Arbeit liegt vor:
A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas (2012)

Epigenetic disruption of tumor suppressor genes is frequently involved in tumorigenesis. We identified a novel 19q13 KRAB domain-containing zinc finger protein, ZNF545/ZFP82, broadly expressed in normal tissues but downregulated in multiple tumor cell lines. The ZNF545 promoter contains a CpG island, which is frequently methylated in cell lines. The transcriptional silencing of ZNF545 could be reversed by pharmacologic or genetic demethylation, indicating direct epigenetic silencing. ZNF545 was also frequently methylated in multiple primary tumors of nasopharyngeal, esophageal, lung, gastric, colon, and breast, but rarely in normal epithelial tissues and paired normal tissues. ZNF545 is located in the nucleus and mainly sequestered in nucleoli, functioning as a repressor. ZNF545 is able to repress NF-κB and AP-1 signaling pathways, whereas ectopic expression of ZNF545 in silenced tumor cells significantly inhibited their growth and induced apoptosis. Functional studies showed that ZNF545 was involved in ribosome biogenesis through inhibiting the activity of rDNA promoter and decreasing cellular protein translation efficiency. Thus, we identified ZNF545 as a novel tumor suppressor inducing tumor cell apoptosis, repressing ribosome biogenesis and target gene transcription. The tumor-specific methylation of ZNF545 could be an epigenetic biomarker for cancer diagnosis.
High-Frequency Spin-Valve Effect in a Ferromagnet-Semiconductor-Ferromagnet Structure Based on Precession of the Injected Spins (2004)

A new mechanism of magnetoresistance, based on tunneling emission of spin-polarized electrons from ferromagnets (FM) into semiconductors (S) and precession of electron spin in the semiconductor layer under external magnetic field, is described. The FM-S-FM structure is considered, which includes very thin heavily doped (delta-doped) layers at FM-S interfaces. At certain parameters the structure is highly sensitive at room temperature to variations of the field with frequencies up to 100 GHz. The current oscillates with the field, and its relative amplitude is determined only by the spin polarizations of FM-S junctions.
Improvement of Gibberellin Efficiency in Prolonging the Citrus Harvest Season by the Surfactant L-77 (1987)

Abstract L-77, a nonionic organo-silicone block copolymer surfactant, significantly increased [ 14 C]GA 3 uptake and physiological effects of GA 3 on ‘Marsh’ seedless grapefruit, as compared with the commonly used surfactant Triton B 1956. Effects on fruit strength at harvest were assessed by testing rheological parameters and evaluating peel color. Corroborating results also were obtained in field trials with ‘Minneola’ tangelo and ‘Clementine’ tangerine. Using L-77, even one single fall application of 1 ppm GA 3 proved commercially effective.
Nesprin-2 Giant (NUANCE) maintains nuclear envelope architecture and composition in skin (2008)

Giant isoforms, encoded by Nesprin-1 (Syne1) and Nesprin-2 (Syne2), are multifunctional actin-binding and nuclear-envelope-associated proteins belonging to the spectrin superfamily. Here, we investigate the function of Nesprin-2 Giant (NUANCE) in skin by generating mice lacking the actin-binding domain of Nesprin-2 (Nesprin-2DeltaABD). This loss results in a slight but significant thickening of the epidermis, which is a consequence of the increased epithelial nuclear size. Nonetheless, epidermal proliferation and differentiation appear normal in the knockout epidermis. Surprisingly, Nesprin-2 C-terminal-isoform expression and nuclear envelope localization were affected in certain tissues. Nuclei of primary dermal knockout fibroblasts and keratinocytes were heavily misshapen, displaying a striking similarity to nuclear deformations characteristic of laminopathies. Furthermore, emerin, the protein involved in the X-linked form of Emery-Dreifuss muscular dystrophy (EDMD), was unevenly distributed along the nuclear envelope in mutant fibroblasts, often forming aggregates in the deformed nuclear envelope areas. Thus, Nesprin-2 is an important scaffold protein implicated in the maintenance of nuclear envelope architecture. Aged knockout fibroblasts readily generated, by alternative splicing and alternative translation initiation, aberrant Nesprin-2 Giant isoforms that lacked an ABD but that were sufficient to restore nuclear shape and emerin localization; this suggests that other regions of Nesprin-2 Giant, potentially including its spectrin repeats, are crucial for these functions.
The Cloning and Expression of Human Deoxyribonuclease II (1998)

We have previously implicated deoxyribonuclease II (DNase II) as an endonuclease responsible for DNA digestion during apoptosis. The full-length human cDNA has now been cloned. The cDNA contains an open reading frame of 1078 bases coding for a 40-kDa protein. This protein is 10 kDa larger than commercially supplied enzyme, which has been proteolytically cleaved at an internal aspartate residue. The gene is located at chromosome 19p13.2, and has no significant homology to other human proteins, but has >30% identity to three predicted genes in Caenorhabditis elegans. To determine whether overexpression of DNase II induces apoptosis in Chinese hamster ovary cells, the cDNA was cotransfected with a plasmid encoding green fluorescent protein. Within 24 h, a significant proportion of green fluorescent protein-positive cells contained condensed chromatin, whereas vector-only controls remained viable. Considering that DNase II is normally active only at low pH, it was surprising that transfection induced chromatin condensation. To confirm that transfection was not activating another endonuclease, cells were incubated with the caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp-(O-methyl)-fluoromethylketone; this failed to inhibit chromatin condensation induced by DNase II. These results demonstrate that DNase II acts downstream of caspase activation and that it may be activated by an as yet unknown mechanism to induce DNA digestion during apoptosis.
Identification of a Functional 2-keto-<i>myo</i>-Inositol Dehydratase Gene of<i>Sinorhizobium fredii</i>USDA191 Required for<i>myo</i>-Inositol Utilization (2006)

Sinorhizobium fredii USDA191 is a Gram-negative bacterium capable of forming nitrogen-fixing nodules on soybean roots. The USDA191 idhA gene encoding myo-inositol dehydrogenase, an enzyme necessary for myo-inositol utilization, is known to be involved in competitive nodulation and nitrogen fixation. In Bacillus subtilis, myo-inositol dehydrogenase catalyzes the first step of the myo-inositol catabolic pathway. Recently iolE was identified as the gene encoding 2-keto-myo-inositol dehydratase, which catalyzes the second step in the pathway. Here we report the presence of 2-keto-myo-inositol dehydratase activity in free-living USDA191 cells cultured in a medium containing myo-inositol. An iolE ortholog was cloned from USDA191. USDA191 iolE was expressed in Escherichia coli as a His(6)-tag fusion and purified to exhibit 2-keto-myo-inositol dehydratase activity. Inactivation of USDA191 iolE led to defective myo-inositol utilization. USDA191 iolE partially complemented a B. subtilis iolE deficient mutant. These results suggest that S. fredii USDA191 utilizes a myo-inositol catabolic pathway, analogous to that of B. subtilis, involving at least idhA and iolE.
The natural history of CIN I lesions. (1998)

The published literature indicates 11% of CIN I lesions on average progress to a higher grade dysplasia and the remainder either regress or persist. Reliable markers of disease outcome are yet to be identified. A longitudinal study of 342 women referred for colposcopic examination of a CIN I detected by a screening Pap test, and classified by the colposcopic impression and Pap test at that exam as </= CIN 1 was designed to identify predictors of disease outcome. The cohort was comprised of 220 women who satisfactorily completed the study and whose disease was neither biopsied or treated at the initial examination. All had HPV DNA testing by PCR, and were followed with interval colposcopic examinations and repeat Pap tests for a limited time period. The initial HPV DNA status and a number of measured clinico-pathological and risk factor variables were analyzed to identify outcome predictors. All underwent a biopsy either at the conclusion of the study or because their disease was considered to have progressed during the follow up period. Biopsy confirmed progression to CIN II/III occurred in 41 (18.6%), persistence of CIN I/Condyloma in 41 (18.6%), and regression to <CIN I/Condyloma in 138 (62.7%). HPV DNA positivity and current, oral contraceptive use were the only independent predictors of progression when age at diagnosis, the number of follow up visits, and time to progression were controlled. Predictors of persistent and regressed disease were not identified. The study highlights a clinical role for HPV testing in the colposcopic management of CIN I lesions. Oral contraceptives may promote progression by regulating the oncogenic sequences of the HPV.
The Role Of Audio And Tags In Music Mood Prediction: A Study Using Semantic Layer Projection. (2013)

[TODO] Add abstract here.
Dynamic optical soliton communication (1990)

Digitally coded optical solitons at 5 and 10 Gb/s have been successfully transmitted over 400 and 300 km, respectively, using erbium-doped fiber amplifiers and repeaters. The soliton pulse source is a gain-switched distributed-feedback laser diode with spectral windowing. The repeater spacing for the 10-Gb/s transmission with an input soliton of A=1.4 is 25 km, which is extended to 50 km for 5-Gb/s transmission with an input soliton of N=1.8-2.0.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Influence of Temperature on the Efficacy of 2-Phenoxyethanol as a Preservative for Adsorbed Diphtheria-Purified Pertussis-Tetanus Combined Vaccine. (2002)

The efficacy of two antimicrobial preservatives, 2-phenoxyethanol (2-PE) and Thimerosal, was compared in adsorbed diphtheria-purified pertussis-tetanus combined vaccine (DPT vaccine). Thimerosal had strong microbicidal activity against Gram-positive bacteria, Gram-negative bacteria, yeast and fungi at 25C and 4C. 2-PE also had microbicidal activity against these microorganisms, only had microbistatic activity against fungi at 4C. Neither 2-PE nor Thimerosal affected the potency or toxicity of the DPT vaccine. These data suggest that 2-PE has weaker antimicrobial activity than Thimerosal against yeast and fungi in DPT vaccine at low temperatures.
Relations of Epicardial Adipose Tissue Measured by Multidetector Computed Tomography to Components of the Metabolic Syndrome Are Region-Specific and Independent of Anthropometric Indexes and Intraabdominal Visceral Fat (2008)

A simple measurement of EAT thickness in the left atrioventricular groove may provide a more accurate assessment of metabolic risk associated with EAT, which could not be accounted for by anthropometric indexes and intraabdominal visceral fat.
Molecular Determinants of Artemisinin Resistance in k13 Gene of Plasmodium falciparum (2015)

Artemisinin-based combination therapy (ACT) is the first-line therapy in most malaria endemic countries. An impressive 47% reduction in the global mortality rate between 2000 and 2013 has been achieved by ACT and artemisinin (ART) monotherapy. However, artemisinin resistance (AR) by Plasmodium falciparum (P. falciparum) is now prevalent across south-east Asia (SEA). AR is indicated by delayed parasite clearance of more than 3 days after standard ART treatment and reduced in vitrosusceptibility. Recent work has shown association of AR with mutations in the propeller domain of the kelch gene on chromosome 13 (PF3D7_1343700, k13gene) of P. falciparum. The C580Y mutation of thek13gene is highly prevalent in Cambodia, Myanmar and eastern and western Thailand, while the F446I mutation is predominant in the China-Myanmar border regions as well as in Myanmar. AR has not reached India and Africa, where non-synonymous mutations not associated with delayed parasite clearance are present. Because the location of Myanmar is central between SEA and Africa, a country-specific strategy for Myanmar Artemisinin Resistance Containment (MARC) is necessary. Moreover, regular periodic tracking of prevalent molecular determinants such as C580Y and F446I mutations will be beneficial.
Inhaled Hydrogen Sulfide Prevents Neurodegeneration and Movement Disorder in a Mouse Model of Parkinson's Disease (2010)

Parkinson's disease is one of the major neurodegenerative disorders. Neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) can cause Parkinson's disease-like symptoms and biochemical changes in humans and animals. Hydrogen sulfide (H(2)S) has been shown to protect neurons. The goal of this study was to examine the effects of inhaled H(2)S in a mouse model of Parkinson's disease induced by MPTP. Male C57BL/6J mice received MPTP at 80 mg/kg and breathed air with or without 40 ppm H(2)S for 8 h/day for 7 days. Administration of MPTP induced movement disorder and decreased tyrosine hydroxylase (TH)-containing neurons in the substantia nigra and striatum in mice that breathed air. Inhalation of H(2)S prevented the MPTP-induced movement disorder and the degeneration of TH-containing neurons. Inhaled H(2)S also prevented apoptosis of the TH-containing neurons and gliosis in nigrostriatal region after administration of MPTP. The neuroprotective effect of inhaled H(2)S after MPTP administration was associated with upregulation of genes encoding antioxidant proteins, including heme oxygenase-1 and glutamate-cysteine ligase. These observations suggest that inhaled H(2)S prevents neurodegeneration in a mouse model of Parkinson's disease induced by MPTP, potentially via upregulation of antioxidant defense mechanisms and inhibition of inflammation and apoptosis in the brain.