gebhart/patrepeval huggingface dataset:
Human papillomavirus 16 E7 protein is associated with the nuclear matrix. (1991)

The cellular localization of the human papillomavirus (HPV)-16 E7 gene product in the cell lines CaSki and SiHa has been determined by both biochemical and immunocytochemical methods. These measurements show E7 to be localized in the cell nucleus, specifically with the nonchromatin nuclear structure or nuclear matrix. This localization of E7 required an unambiguous fractionation of the nuclear constituents. This was achieved by using a gentle sequential fractionation procedure to prepare the scaffold consisting of the nuclear matrix and intermediate filaments (NM-IF). Chromatin was cleaved with nuclease and the resulting nucleosomes eluted with 0.25 M ammonium sulfate. Immunostaining of cells after this extraction procedure with monoclonal antibodies (mAbs) to E7 revealed a fine grained, punctate nuclear fluorescence in CaSki and SiHa, which was absent in normal cervical keratinocytes and the HPV-negative cell line C33.1. Western blots of cell fractions with these mAbs showed that E7 was localized in the NM-IF fraction in SiHa and CaSki but was not detected in HPV-negative cells. A second protein of slightly higher mobility is identified by these antisera in HPV-16-containing cells. The data suggest that the previous inability to directly visualize E7 by immunocytology is due to the masking of epitopes by cellular components and not to low levels of protein.
Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing (2001)

The low molecular weight fraction of tomato plants inoculated with potato spindle tuber viroid (PSTVd) contains a population of short PSTVd-specific RNAs of either polarity. The main constituents were RNAs of 22 and 23 nt representing different domains of the viroid genome. The occurrence of such distinct RNA species indicated that the nuclear replicating PSTVd RNA induces post-transcriptional gene silencing. The short RNAs were slightly more abundant at 30 days post-inoculation than at later stages and were present in plants infected with a mild, severe or lethal isolate of PSTVD: There was no apparent correlation between the quantity of small PSTVd-specific RNAs and the degree of virulence of the viroid isolate.
Advances in sensitivity encoding with arbitrary k‐space trajectories (2001)

New, efficient reconstruction procedures are proposed for sensitivity encoding (SENSE) with arbitrary k-space trajectories. The presented methods combine gridding principles with so-called conjugate-gradient iteration. In this fashion, the bulk of the work of reconstruction can be performed by fast Fourier transform (FFT), reducing the complexity of data processing to the same order of magnitude as in conventional gridding reconstruction. Using the proposed method, SENSE becomes practical with nonstandard k-space trajectories, enabling considerable scan time reduction with respect to mere gradient encoding. This is illustrated by imaging simulations with spiral, radial, and random k-space patterns. Simulations were also used for investigating the convergence behavior of the proposed algorithm and its dependence on the factor by which gradient encoding is reduced. The in vivo feasibility of non-Cartesian SENSE imaging with iterative reconstruction is demonstrated by examples of brain and cardiac imaging using spiral trajectories. In brain imaging with six receiver coils, the number of spiral interleaves was reduced by factors ranging from 2 to 6. In cardiac real-time imaging with four coils, spiral SENSE permitted reducing the scan time per image from 112 ms to 56 ms, thus doubling the frame-rate.
Wavelet analysis of voluntary cough sound in patients with respiratory diseases. (2008)

Changes in the characteristics of the cough sound may refer to some specific pathological processes and their evolution. In this pilot study we analyzed voluntary cough sound properties in subjects with asthma bronchiale (AB) and chronic obstructive pulmonary disease (COPD) and discriminated them from the control cough sound in healthy subjects. The wavelet transform was used due to a nonstationarity of cough sound recordings. The duration of cough sound was longer during pathological conditions. The longest duration and the highest power of the cough sound were found in COPD. In AB patients, higher frequencies were detected compared with chronic bronchitis and the power of cough sound was shifted to a higher frequency range compared with control coughs. Cough sounds were classified using discriminant analysis with a correct classification rate of about 85-90 %. The method of cough analysis enables an objective quantification of voluntary cough sound with a useful diagnostic and prognostic value.
Lidocaine by Enzyme Immunoassay (1978)

Journal Article Lidocaine by Enzyme Immunoassay Get access Clifford B. Walberg Clifford B. Walberg Toxicology Laboratory, Los Angeles County - University of Southern California Medical Center and the University of Southern California School of Medicine, Los Angeles, CA 90033 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Analytical Toxicology, Volume 2, Issue 4, July-August 1978, Pages 121–123, https://doi.org/10.1093/jat/2.4.121 Published: 01 July 1978 Article history Received: 31 March 1978 Published: 01 July 1978
Evaluation of Three Procedures for the Preparation ofLeukocyte-Poor and Leukocyte-Free Red Blood Cellsfor Transfusion (1980)

Three methods of leukocyte deprivation of blood for transfusion have been evaluated. Filtration of relatively fresh packed red cells (up to 5 days old) through Erypur filters appears to be the method of choice for the preparation of leukocyte-free red cells, used to prevent the production of antileukocyte antibodies in nonimmunized, nontransfused patients undergoing repeated blood transfusions. Double dextran sedimentation plus saline washings also yields leukocyte-free red cells, although with a lower frequency, and represents an alternative to Erypur filtration, especially because of the lower cost and no need of special equipment. Imugard filtration appears to be a simple and effective way for preparing leukocytepoor red blood cells. For all the three procedures, results are definitely better when bufly coatfree packed red cell units are processed. In a given hospital the choice of the technique(s) for the preparation of leukocyte-poor (free) red blood cells for transfusion depends on a number of factors, such as type of patients to be transfused (immunized or nonimmunized, small children or boys and adults), aim of the procedure (prevention of the febrile transfusion reaction or prevention of antileukocyte antibody production), continuous availability of materials, cost, length and easiness of the procedure; these three latter parameters are in turn related to a number of local situations and facilities.
Identification of Transcriptional Regulatory Elements in Human Mitochondrial DNA by Linker Substitution Analysis (1989)

Human mitochondrial DNA contains two major promoters, one for transcription of each strand of the helix. Previous mapping and mutagenesis data have localized these regulatory elements and have suggested regions important to their function. In order to define, at high resolution, the sequences critical for accurate and efficient transcriptional initiation, a linker substitution analysis of the entire promoter region was performed. Each promoter was shown to consist of approximately 50 base pairs comprising two functionally distinct elements. These and previous data strongly support a mode of transcription initiation requiring minimal sequences surrounding the initiation sites that are likely interactive with core polymerase and upstream regulatory domains capable of binding a transcription factor that modulates the efficiency of transcription initiation. Furthermore, in at least one case, this upstream regulatory domain is capable of operating bidirectionally.
Deletion analysis of tumor and urinary DNA to detect bladder cancer: Urine supernatant versus urine sediment (2007)

The accumulation of genetic alterations plays a role in the evolution of bladder cancer. These changes can be detected in the urine by DNA analysis of the cells exfoliated from the bladder wall enabling us to detect bladder cancer. The urine supernatant, besides the urine sediment, contains DNA, however in a much smaller amount. The origin of DNA in these two fractions is probably different. Our aim was to evaluate which fraction (supernatant or sediment) provides more reliable results in detecting tumors. We analyzed blood, urine and tumor samples taken from 80 individuals (44 patients with bladder cancer, 20 control patients and 16 healthy volunteers) by using 12 microsatellite markers mapped on 6 chromosomes. Microsatellite alterations were detected in the urine sediment and supernatant in 86% of the cancer cases. Urine sediment alone had a sensitivity of 68%, while urine supernatant alone indicated aberrations in 80% of the tumors. In the superficial (Ta/T1) cases, a considerable difference in sensitivity, 84 vs. 67%, was found between the two fractions in favor of urine supernatant. We also detected deletions in the control groups, although in a much lower proportion. Loss of the 16q24 chromosomal region showed a significant correlation with tumor stage (p=0.02). Microsatellite analysis of the urine is an efficient and noninvasive molecular method to detect bladder cancer. The analysis of free DNA in the urine supernatant provides a higher detection rate. The marker on the chromosomal region 16q24 is suggested to have a prognostic value.
Biochemical Identification of Xenopus Pumilio as a Sequence-specific Cyclin B1 mRNA-binding Protein That Physically Interacts with a Nanos Homolog, Xcat-2, and a Cytoplasmic Polyadenylation Element-binding Protein (2001)

Translational activation of dormant cyclin B1 mRNA stored in oocytes is a prerequisite for the initiation or promotion of oocyte maturation in many vertebrates. Using a monoclonal antibody against the domain highly homologous to that of Drosophila Pumilio, we have shown for the first time in any vertebrate that a homolog of Pumilio is expressed in Xenopus oocytes. This 137-kDa protein binds to the region including the sequence UGUA at nucleotides 1335-1338 in the 3'-untranslated region of cyclin B1 mRNA, which is close to but does not overlap the cytoplasmic polyadenylation elements (CPEs). Physical in vitro association of Xenopus Pumilio with a Xenopus homolog of Nanos (Xcat-2) was demonstrated by a protein pull-down assay. The results of immunoprecipitation experiments showed in vivo interaction between Xenopus Pumilio and CPE-binding protein (CPEB), a key regulator of translational repression and activation of mRNAs stored in oocytes. This evidence provides a new insight into the mechanism of translational regulation through the 3'-end of mRNA during oocyte maturation. These results also suggest the generality of the function of Pumilio as a translational regulator of dormant mRNAs in both invertebrates and vertebrates.
A Randomized Double-Blind Prospective Study of the Efficacy of Pulsed Electromagnetic Fields for Interbody Lumbar Fusions (1990)

A randomized double-blind prospective study of pulsed electromagnetic fields for lumbar interbody fusions was performed on 195 subjects. There were 98 subjects in the active group and 97 subjects in the placebo group. A brace containing equipment to induce an electromagnetic field was applied to patients undergoing interbody fusion in the active group, and a sham brace was used in the control group. In the active group there was a 92% success rate, while the control group had a 65% success rate (P greater than 0.005). The effectiveness of bone graft stimulation with the device is thus established.
Alternate splicing produces a novel cyclin D1 transcript. (1995)

Using Northern blotting and PCR analysis of cDNA derived from a range of cell lines and tissues, alternate splicing of the cyclin D1 gene (CCND1) mRNA has been demonstrated. The variant transcript shows no splicing at the downstream exon 4 boundary, encoding a protein with an altered carboxy-terminal domain. Investigation of mRNA extracted from mononuclear cells, lung tumour and normal tissue suggests that both transcripts are invariably expressed. However, splicing to produce the two forms of mRNA is modulated, in the heterozygote, by a frequent A/G polymorphism located within the splice donor region of exon 4. Preliminary analysis of patients with resectable non-small cell lung cancer suggests that genotype is associated with shortened event free survival and greater risk of local relapse.
1006 (2012)

Introduction: Vapotherm (VPT), a high flow oxygen delivery system, has been extensively studied in the pediatric population, but data in adult critically ill patients (pts) is limited. Multiple theoretical cited advantages of VPT exist, including improved nutrition and increased tolerance of respiratory support. However, no data exists whether VPT decreases pts length of stay (LOS) in Adult Intensive Care Units (ICU). Hypothesis: VPT use will decrease ICU length of stay (ICU LOS) in a mixed Medical-Surgical Academic ICU. Methods: The Project IMPACT database was utilized to identify patients on VPT, VPT + Mechanical Ventilation (MV), VPT + non-invasive ventilation (NIV) and VPT + NIV + MV from 1/1/07 to 3/1/11 in a mixed Academic Medical-Surgical ICU. Besides routine demographic data, Apache II, ICU LOS, mortality and cormobidities including CHF, CAD, DM, COPD, HTN, CVA were recorded. Data was analyzed using multiple regression analysis. Results: 4871 patients were included in the study. Twenty-eight patients were on VPT alone, 60 pts on VPT and MV, 22 on VPT and NIV and 51 on a combination of all three. There was a significant difference in ICU LOS between the assisted ventilation groups. By univariate analysis VPT only patients had a significantly less ICU LOS. Average ICU LOS for VPT pts was 4 days (+/- 2.77), VPT+ MV 11.64 days (+/- 9.39), VPT + NIV 4.4 days (+/- 3.12), VPT + MV + NIV 13.62 days (+/- 9.0) with a p < 0.01. After adjusting for clinical severity using APACHE II scores, the difference in ICU LOS was no longer significant. Conclusions: The use of VPT doesnot decrease ICU LOS when a multivariate analysis includes APACHE II score. The utility of this modality in the ICU needs to be studied more extensively.
Effects of Staggered Magnetic Field on Entanglement in the Anisotropic XY Model (2006)

我们调查效果蹒跚磁性在各向异性的 XY 模型在热纠纷上删除。为二地点的案例的纠纷的分析结果被获得。为甚至地点的一般案例，我们证明当各向异性的参数是零时，在有一个蹒跚的磁场的 XY 模型的纠纷与一个一致磁场与那一样。
Visual-Inertial-Aided Navigation for High-Dynamic Motion in Built Environments Without Initial Conditions (2011)

In this paper, we present a novel method to fuse observations from an inertial measurement unit (IMU) and visual sensors, such that initial conditions of the inertial integration, including gravity estimation, can be recovered quickly and in a linear manner, thus removing any need for special initialization procedures. The algorithm is implemented using a graphical simultaneous localization and mapping like approach that guarantees constant time output. This paper discusses the technical aspects of the work, including observability and the ability for the system to estimate scale in real time. Results are presented of the system, estimating the platforms position, velocity, and attitude, as well as gravity vector and sensor alignment and calibration on-line in a built environment. This paper discusses the system setup, describing the real-time integration of the IMU data with either stereo or monocular vision data. We focus on human motion for the purposes of emulating high-dynamic motion, as well as to provide a localization system for future human-robot interaction.
The Small Heat Shock Protein αB-Crystallin Negatively Regulates Cytochrome c- and Caspase-8-dependent Activation of Caspase-3 by Inhibiting Its Autoproteolytic Maturation (2001)

Caspases are universal effectors of apoptosis. The mitochondrial and death receptor pathways activate distinct apical caspases (caspase-9 and -8, respectively) that converge on the proteolytic activation of the downstream executioner caspase-3. Caspase-9 and -8 cleave procaspase-3 to produce a p24 processing intermediate (composed of its prodomain and large subunit), which then undergoes autoproteolytic cleavage to remove the prodomain from the active protease. Recently, several heat shock proteins have been shown to selectively inhibit the mitochondrial apoptotic pathway by disrupting the activation of caspase-9 downstream of cytochrome c release. We report here that the small heat shock protein alphaB-crystallin inhibits both the mitochondrial and death receptor pathways. In S-100 cytosolic extracts treated with cytochrome c/dATP or caspase-8, alphaB-crystallin inhibits the autoproteolytic maturation of the p24 partially processed caspase-3 intermediate. In contrast, neither the closely related small heat shock protein family member Hsp27 nor Hsp70 inhibited the maturation of the p24 intermediate. We also demonstrate that alphaB-crystallin co-immunoprecipitates with the p24 partially processed caspase-3 in vivo. Taken together, our results demonstrate that alphaB-crystallin is a novel negative regulator of apoptosis that acts distally in the conserved cell death machinery by inhibiting the autocatalytic maturation of caspase-3.
Proliferation and invasion: Plasticity in tumor cells (2005)

Invasive and proliferative phenotypes are fundamental components of malignant disease, yet basic questions persist about whether tumor cells can express both phenotypes simultaneously and, if so, what are their properties. Suitable in vitro models that allow characterization of cells that are purely invasive are limited because proliferation is required for cell maintenance. Here, we describe glioblastoma cells that are highly invasive in response to hepatocyte growth factor/scatter factor (HGF/SF). From this cell population, we selected subclones that were highly proliferative or displayed both invasive and proliferative phenotypes. The biological activities of invasion, migration, urokinase-type plasminogen activation, and branching morphogenesis exclusively partitioned with the highly invasive cells, whereas the highly proliferative subcloned cells uniquely displayed anchorage independent growth in soft agar and were highly tumorigenic as xenografts in immune-compromised mice. In response to HGF/SF, the highly invasive cells signal through the MAPK pathway, whereas the selection of the highly proliferative cells coselected for signaling through Myc. Moreover, in subcloned cells displaying both invasive and proliferative phenotypes, both signaling pathways are activated by HGF/SF. These results show how the mitogen-activated protein kinase and Myc pathways can cooperate to confer both invasive and proliferative phenotypes on tumor cells and provide a system for studying how transitions between invasion and proliferation can contribute to malignant progression.
Rhodium Complex-Catalyzed Pauson−Khand-Type Reaction with Aldehydes as a CO Source (2002)

With aldehydes as a CO source under solvent-free conditions, rhodium complex efficiently catalyzed an intramolecular carbonylative alkene-alkyne coupling (Pauson-Khand-type reaction) and various bicyclic enones were obtained in high yield. Experiments under argon flow and a 13C-labeling experiment suggested that almost no free carbon monoxide was generated in this reaction. When noncationic rhodium complex with chiral phosphine was used as a chiral catalyst, the reaction proceeded enantioselectively to give various chiral cyclopentenones in up to 90% ee under solvent-free conditions.
Genomic Organization and Molecular Characterization of SM1, a Temperate Bacteriophage ofStreptococcus mitis (2003)

The direct binding of Streptococcus mitis to human platelets is mediated in part by two proteins (PblA and PblB) encoded by a lysogenic bacteriophage (SM1). Since SM1 is the first prophage of S. mitis that has been identified and because of the possible role of these phage-encoded proteins in virulence, we sought to characterize SM1 in greater detail. Sequencing of the SM1 genome revealed that it consisted of 34,692 bp, with an overall G+C content of 39 mol%. Fifty-six genes encoding proteins of 40 or more amino acids were identified. The genes of SM1 appear to be arranged in a modular, life cycle-specific organization. BLAST analysis also revealed that the proteins of SM1 have homologies to proteins from a wide variety of lambdoid phages. Bioinformatic analyses, in addition to N-terminal sequencing of the proteins, led to the assignment of possible functions to a number of proteins, including the integrase, the terminase, and two major structural proteins. Examination of the phage structural components indicates that the phage head may assemble using stable multimers of the major capsid protein, in a process similar to that of phage r1t. These findings indicate that SM1 may be part of a discrete subfamily of the Siphoviridae that includes at least phages r1t of Lactococcus lactis and SF370.3 of Streptococcus pyogenes.
Preimage and Pseudo-Collision Attacks on Step-Reduced SM3 Hash Function. (2012)

SM3 [11] is the Chinese cryptographic hash standard which was announced in 2010 and designed by Wang et al.. It is based on the Merkle-Damgard design and its compression function can be seen as a block cipher used in DaviesMeyer mode. It uses message block of length 512 bits and outputs hash value of length 256 bits. This paper studies the security of SM3 hash function against preimage attack and pseudo-collision attack. We propose preimage attacks on 29-step and 30-step SM3, and pseudo-preimage attacks on 31-step and 32-step SM3 out of 64 steps. The complexities of these attacks are 2245 29-step operations, 2251.1 30-step operations, 2245 31-step operations and 2251.1 32-step operations, respectively. These (pseudo) preimage attacks are all from the first step of the reduced SM3. Meanwhile, these (pseudo) preimage attacks can be converted into pseudo-collision attacks on SM3 reduced to 29 steps, 30 steps, 31 steps and 32 steps with complexities of 2122, 2125.1, 2122 and 2125.1 respectively. As far as we know, the previously best known preimage attacks on SM3 cover 28 steps (from the first step) and 30 steps (from the 7-th step), and there is no publicly published result on (pseudo) collision attack on SM3.