gebhart/patrepeval huggingface dataset:
Statistical Similarities between Transcriptomics and Quantitative Shotgun Proteomics Data (2007)

If the large collection of microarray-specific statistical tools was applicable to the analysis of quantitative shotgun proteomics datasets, it would certainly foster an important advancement of proteomics research. Here we analyze two large multidimensional protein identification technology datasets, one containing eight replicates of the soluble fraction of a yeast whole-cell lysate and one containing nine replicates of a human immunoprecipitate, to test whether normalized spectral abundance factor (NSAF) values share substantially similar statistical properties with transcript abundance values from Affymetrix GeneChip data. First we show similar dynamic range and distribution properties of these two types of numeric values. Next we show that the standard deviation (S.D.) of a protein's NSAF values was dependent on the average NSAF value of the protein itself, following a power law. This relationship can be modeled by a power law global error model (PLGEM), initially developed to describe the variance-versus-mean dependence that exists in GeneChip data. PLGEM parameters obtained from NSAF datasets proved to be surprisingly similar to the typical parameters observed in GeneChip datasets. The most important common feature identified by this approach was that, although in absolute terms the S.D. of replicated abundance values increases as a function of increasing average abundance, the coefficient of variation, a relative measure of variability, becomes progressively smaller under the same conditions. We next show that PLGEM parameters were reasonably stable to decreasing numbers of replicates. We finally illustrate one possible application of PLGEM in the identification of differentially abundant proteins that might potentially outperform standard statistical tests. In summary, we believe that this body of work lays the foundation for the application of microarray-specific tools in the analysis of NSAF datasets.
Caspase-10 is an initiator caspase in death receptor signaling (2001)

A role for caspase-10, previously implicated in the autoimmune lymphoproliferative syndrome, in death receptor signaling has not been directly shown. Here we show that caspase-10 can function independently of caspase-8 in initiating Fas- and tumor necrosis factor-related apoptosis-inducing ligand-receptor-mediated apoptosis. Moreover, Fas crosslinking in primary human T cells leads to the recruitment and activation of caspase-10. Fluorescent resonance energy transfer analysis indicates that the death-effector domains of caspase-8 and -10 both interact with the death-effector domain of FADD. Nonetheless, we find that caspase-8 and -10 may have different apoptosis substrates and therefore potentially distinct roles in death receptor signaling or other cellular processes.
<i>Protease nexin-1</i> is expressed at the mouse met-/mesencephalic junction and FGF signaling regulates its promoter activity in primary met-/mesencephalic cells (1997)

The expression pattern of the serine protease inhibitor gene Protease nexin-1 (PN-1) has been analyzed by in situ hybridization during embryonic nervous system development. PN-1 was found to be specifically expressed at the junction between the mes- and metencephalon (mid- and hindbrain). Transgenic embryos expressing the bacterial lacZ gene under the control of different fragments of the PN-1 upstream regulatory region were used to demarcate an enhancer sufficient for expression at this putative segmental border. Primary cell cultures derived from the embryonic neural tube at the level of the met-/mesencephalic junction were used to demonstrate a specific effect on transcriptional activity by basic fibroblast growth factor and Engrailed transcription factors, providing evidence that PN-1 is a target gene of these factors. The results of this study place PN-1 into the signaling cascade(s) considered to be important for the development of this junction and suggest a role for PN-1 in the establishment or maintenance of the differences between these adjacent neuromeres.
Hydrogels with Controlled, Surface Erosion Characteristics from Self-Assembly of Fluoroalkyl-Ended Poly(ethylene glycol) (2001)

Poly(ethylene glycol) (PEG) (M_w = 6k, 10k, and 20k g/mol) terminated at both ends by hydrophobic fluoroalkyl segments (−(CH_2)_2C_nF_(2n+1), n = 6, 8, or 10) was synthesized and demonstrated to self-assemble into hydrogels with phase behavior and mechanical and erosion properties that can be systematically varied by molecular design. With increasing fluoroalkyl length relative to PEG length, the phase behavior of these polymers in aqueous solution changes from the single-phase behavior of familiar associative thickeners, to sol−gel coexistence, to precipitation. For those polymers that exhibit sol−gel coexistence, the equilibrium gel concentration (or swelling ratio of the gel phase) and the modulus of the gel phase are governed by the length of the PEG midblock, whereas the relaxation time is determined by the hydrophobe length. The erosion characteristics of these hydrogels correlate with their phase behavior. The gels of sol−gel coexisting species exhibit surface erosion in an open system with a slow dissolution rate controlled by the end-group length; in contrast, hydrogels from polymers that show single-phase behavior exhibit bulk erosion that is relatively fast. Therefore, the molecular structure of this class of polymers produces hydrogels whose mechanical and erosion properties can be tailored for desired applications. Based on the established biocompatibility of PEG, the degree to which the characteristics of the gel phases can be tailored, and the surface erosion characteristics that can be achieved, these materials might have applications in implantable drug-release depots.
The Ariadne Infrastructure for Managing and Storing Metadata (2009)

Reusing digital resources for learning has been a goal for several decades, driven by potential time savings and quality enhancements. Although the rapid development of Web-based learning has increased opportunities for reuse significantly, managing learning objects and making them accessible still entails many challenges. This article presents and analyzes the standards-based Ariadne infrastructure for managing learning objects in an open and scalable architecture. The architecture supports the integration of learning objects in multiple, distributed repository networks. The authors capture lessons learned in four architectural patterns.
Differential Module 에 대한 연구 (1975)

In this paper, we define a differential module and study its properties. In section 2, as for propositions, we research some properties, directsum, isomorphism of factorization, exact sequence of derived modules. And then as for theorem, I try to present the following statement, if the sequence of homomorphisms of differential modules is exact. Then the sequence of homomorphisms of Z(X) is exact, also the sequence of homomorphisms of Z`(X) is exact. According to the theorem, as for Lemma, we consider commutative diagram between exact sequence of Z(X) and exact sequence of Z`(X). As an immediate consequence of this theorem, we obtain the following result. If M is an arbitrary module and the sequence of homomorphisms of the modules Z(X) is exact, then the sequence of their tensor products with the trivial endomorphism is semi-exact.
Direct yaw-moment control of electric vehicle based on cornering stiffness estimation (2005)

In this paper, novel direct yaw-moment control (DYC) with road condition estimation and anti-slip control is proposed for electric vehicles. An inner-loop observer controls the vehicle traction, and an outer-loop controller stabilizes the yawing motion. An immeasurable parameter known as cornering stiffness is estimated from the detected yaw-rate, steering angle, wheel speed and yaw-moment observer output in real time. Thus, the accurate control input can be generated with the estimated parameters. The proposed adaptive control is compared with a conventional robust control on dry and snowy terrain conditions. The experimental results show that the yaw-rate error is properly attenuated by the proposed control algorithm.
Kit: Molecule of Interest for the Diagnosis and Treatment of Mastocytosis and other Neoplastic Disorders (2007)

Kit a type III receptor tyrosine kinase, along with its ligand the stem cell factor, play a critical role in normal cell growth, differentiation, development and survival. Ligand independent activation of kit (dysregulated kit function) has been found to be an important component of oncogenesis in a large number of neoplastic disorders such as systemic mastocytosis, gastro intestinal stromal tumors, germ cell tumors, acute myelogenous leukemia with the disruption of the core binding factor, amongst others. The identification of small molecule inhibitors with activity against Kit, has offered a wider and more effective range of therapeutic options in the treatment of these neoplastic processes. Novel tyrosine kinase inhibitors such as imatinib, nilotinib and dasatinib, have been found to be effective in the management of various subtypes of systemic mastocytosis and gastrointestinal stromal tumors. Non-tyrosine kinase inhibitors like rapamycin, 17-AAG and IMD- 0354 have been added to the therapeutic armamentarium, with the hope that combination therapy might have a synergistic effect, or prevent/delay the development of drug resistance.
Software reduces errors in managing hyperbilirubinemia (2009)

♦ Balaguer A, et al. Arch Dis Child Fetal Neonatal Ed 2009;94:F45-F47[OpenUrl][1][Abstract/FREE Full Text][2].



Software developed to help apply the 2004 AAP guidelines on the management of hyperbilirubinemia in newborns reduced errors and saved time compared with manual application of the
Failure analysis of power electronic devices and their applications under extreme conditions (2016)

Power electronic devices are the core components of modern power converters, not only for normal applications, but also for extreme conditions. Current design of power electronic devices require large redundancies for reliability. This results in huge volume and weight for a large-capacity power converter, especially for some extreme applications. Therefore, to optimize the power density, the reliability of power devices needs to be investigated first in order to obtain the accurate operational margin of a power device. Although much research on device failure analysis has been reported, there still lacks efficient failure evaluation methods. This paper first summarizes the current failure research. Then, a three-step failure analysis method of power electronic devices is proposed as: failure information collection, failure identification and mechanism, and failure evaluation. The physics-based modeling method is emphasized since it has a strong relationship with the device fundamentals. After that, power electronic device applications under extreme conditions are introduced and a design method of device under extreme conditions is proposed based on the thermal equilibrium idea. Finally, the challenges and prospects to improve the power device reliability under extreme conditions are concluded.
dUTP pyrophosphatase as a potential target for chemotherapeutic drug development. (1997)

Aberrant dUTP metabolism plays a critical role in the molecular mechanism of cell killing induced by inhibitors of dihydrofolate reductase and thymidylate synthase. While considerable effort has been directed towards discovering new, more potent inhibitors of these two enzymes, little attention has been given dUTP pyrophosphatase (dUTPase)--the key modulator of cellular dUTP levels--as a potential target for chemotherapeutic drug development. Recent studies have provided evidence that dUTPase is vital for cellular and, in some cases, viral DNA replication. Furthermore, some retroviruses encode dUTPases--a fact which suggests that cellular dUTP metabolism may be more important than previously realized. Here, we briefly review current knowledge of cellular and viral dUTPases and discuss the potential of these enzymes as targets for cancer chemotherapeutic and anti-viral drug development.
Synchronization in human musical rhythms and mutually interacting complex systems (2014)

Though the music produced by an ensemble is influenced by multiple factors, including musical genre, musician skill, and individual interpretation, rhythmic synchronization is at the foundation of musical interaction. Here, we study the statistical nature of the mutual interaction between two humans synchronizing rhythms. We find that the interbeat intervals of both laypeople and professional musicians exhibit scale-free (power law) cross-correlations. Surprisingly, the next beat to be played by one person is dependent on the entire history of the other person's interbeat intervals on timescales up to several minutes. To understand this finding, we propose a general stochastic model for mutually interacting complex systems, which suggests a physiologically motivated explanation for the occurrence of scale-free cross-correlations. We show that the observed long-term memory phenomenon in rhythmic synchronization can be imitated by fractal coupling of separately recorded or synthesized audio tracks and thus applied in electronic music. Though this study provides an understanding of fundamental characteristics of timing and synchronization at the interbrain level, the mutually interacting complex systems model may also be applied to study the dynamics of other complex systems where scale-free cross-correlations have been observed, including econophysics, physiological time series, and collective behavior of animal flocks.
Is Generator Conditioning Causally Related to GAN Performance? (2018)

Recent work (Pennington et al, 2017) suggests that controlling the entire distribution of Jacobian singular values is an important design consideration in deep learning. Motivated by this, we study the distribution of singular values of the Jacobian of the generator in Generative Adversarial Networks (GANs). We find that this Jacobian generally becomes ill-conditioned at the beginning of training. Moreover, we find that the average (with z from p(z)) conditioning of the generator is highly predictive of two other ad-hoc metrics for measuring the 'quality' of trained GANs: the Inception Score and the Frechet Inception Distance (FID). We test the hypothesis that this relationship is causal by proposing a 'regularization' technique (called Jacobian Clamping) that softly penalizes the condition number of the generator Jacobian. Jacobian Clamping improves the mean Inception Score and the mean FID for GANs trained on several datasets. It also greatly reduces inter-run variance of the aforementioned scores, addressing (at least partially) one of the main criticisms of GANs.
How do you hire auxiliaries? (1978)

Theodore Roosevelt gives his opinion on socialism and global politics in his editorial, "The Liberty Loan and the Pro German," published in 1917 in the Kansas City Star .
The 'Beijing clinical database' on severe acute respiratory syndrome patients: its design, process, quality control and evaluation (2004)

目的 建立北京市严重急性呼吸综合征(SARS)临床诊断病例资料数据库,为相关临床研究提供坚实基础.方法由北京市SARS救治指挥中心组织有关专家设计,分为首诊、生命体征、症状体征、治疗、实验室检查、住院花费6个分库,共包含686个项目.由医护人员经培训后采用统一的专用录入程序进行录入.然后经过(1)专用程序检查验收;(2)5%病历逐项核对;(3)转院病历链接;(4)文字信息编码转换;(5)标准数据库结构转化;(6)计算机程序依据2003年5月3日卫生部标准核实诊断;(7)剔除不合格病例等步骤,最终形成数据库.结果数据库最终纳入被核实的临床诊断病例2148例,资料完整病例1291例.全部病例和资料完整病例比较结果表明:两者在性别、年龄、职业和居住地构成上几乎完全相同,发病时间曲线近于重合;除少数首诊指标外,完整病例各项指标的数据完整率与全部病例无明显差异.数据库中,首诊信息数据完整率 73%～100%;主要症状体征信息数据完整率接近90%;各种药物和氧气治疗信息的数据完整率均近100%;生命体征信息中体温和脉搏数据完整率分别为98%和90%;转归信息完整率100%,住院花费信息完整率98%.结论北京市SARS临床病历数据库所收录的病例数量较完整,且其中的资料完整病例对全部病例具有很好的代表性;临床基本指标的数据完整情况总体上令人满意,适宜开展相关临床研究。
Pushing the envelope - aside [speech recognition (2005)

Despite successes, there are still significant limitations to speech recognition performance, particularly for conversational speech and/or for speech with significant acoustic degradations from noise or reverberation. For this reason, authors have proposed methods that incorporate different (and larger) analysis windows, which are described in this article. Note in passing that we and many others have already taken advantage of processing techniques that incorporate information over long time ranges, for instance for normalization (by cepstral mean subtraction as stated in B. Atal (1974) or relative spectral analysis (RASTA) based in H. Hermansky and N. Morgan (1994)). They also have proposed features that are based on speech sound class posterior probabilities, which have good properties for both classification and stream combination.
Hoe lyk jou vangnet? : let's talk / kom ons praat (2016)

Omdat die natuurlike hulpbron die grondslag van 'n veeboer se besigheid is, is die bestuur daarvan sy alfa en omega. Die ernstige droogte wat ons die afgelope jaar beleef het, het weer gewys dat 'n konserwatiewe benadering ten opsigte van veelading beslis die regte een is.
Regulation of renal ammoniagenesis. Purification and characterization of phosphate-dependent glutaminase from rat kidney. (1976)

Abstract Phosphate-dependent glutaminase can be solubilized from rat kidney mitochondria by treatment with high concentrations of nonionic detergents or by lyophilization in the presence of a borate buffer. Borate promotes a reversible polymerization of this enzyme into a high molecular weight aggregate. Removal of borate to produce the low molecular weight Tris form of glutaminase is associated with a reversible threefold decrease in specific activity. This process makes possible the rapid purification (1000-fold) of this glutaminase by successive gel filtration in each of its molecular weight forms. The purified glutaminase is stable at 3 °C in borate, phosphate buffer for at least 6 months. Activation of this enzyme is not specific and can be achieved by a large number of phosphate-containing compounds including pyrophosphate, nucleotides and sugar phosphates. Nucleotides produced a significantly greater percentage activation of the mitochondrial and borate forms of glutaminase than of the Tris form. In addition, only the former two forms are activated by a large number of carboxylic acids. The specific activities of the borate and Tris forms of glutaminase are also increased by the presence of Triton X-100.
Retinal Arteriolar Diameters and Elevated Blood Pressure: The Atherosclerosis Risk in Communities Study (1999)

Narrowing and other changes in retinal arterioles may reflect damage due to hypertension, which may predict stroke and other cardiovascular diseases independently of blood pressure level. Newly developed quantitative methods of assessing retinal narrowing are used to determine whether this sign is related only to current blood pressure or whether it also independently reflects the effects of previous blood pressure. Retinal photography was performed at the third examination of Atherosclerosis Risk in Communities (ARIC) Study in 1993-1995, and results are presented for the 9,300 nondiabetic participants aged 50-71 years. Generalized narrowing of smaller arterioles was strongly and monotonically related to current blood pressure in men and women, whether they were taking antihypertensive medications or not, and, independent of current blood pressure, was consistently and monotonically related to blood pressure levels measured 3 and 6 years before the retinal assessment. Arteriovenous nicking was also independently related to both current and previous blood pressures. The patterns of association suggested that these signs reflect both transient and persisting structural effects of elevated blood pressure, in agreement with the scant pathologic literature available. The findings suggest that retinal assessment may be useful for research on the microvascular contributions to clinical cardiovascular diseases.
Correlation between Hepatitis B Virus Genotypes and Clinical Outcomes (2012)

Hepatitis B virus (HBV) has been classified into 10 genotypes (A-J) according to genome sequence divergence. HBV genotypes have a distinct geographical distribution. As chronic HBV infection is endemic in the Asian region, genotypes B and C prevail there, and genotypes A and D are mainly found in the western world and Europe. Genotypes A, B, C, and D have been studied most extensively. In Europe and Asia, most patients with genotypes A and B have acute hepatitis B; however, some mutants may tend to cause fulminant hepatitis B. Many studies have indicated that the severity and outcomes of chronic hepatitis B infections are more serious in patients with genotypes C and D than in those with genotypes A and B. Cirrhosis and hepatocellular carcinoma (HCC) are more frequently diagnosed in carriers of genotypes C and D than in those of genotypes A and B. Accumulating evidence indicated that higher plasma HBV DNA levels, infection with HBV genotype C, as well as mutations at 1653T, 1753V, and A1762T/G1764A are independently associated with the risk of HCC in Asian men. However, the therapeutic responses differ with regard to the different HBV genotypes. For example, the response to interferon-α treatment in patients with genotypes A and B was better than that in patients with genotypes C, D, and mixed genotypes. Some studies have shown seroconversion after treatment, i.e., genotypes A and C may switch to genotypes D and B, respectively. Some reports indicated a correlation between the emergence of the hepatitis B e antigen-negative variant in patients with genotypes C and D and worsening of liver injury without sustained response. In order to provide better treatment options for these poorly responding patients, further studies, e.g, novel immunomodulatory therapies, are required. Many studies have shown that HBV genotypes have remarkable clinical and epidemical differences; however, HBV sub-genotypes, mixed genotype infections, and the effect of different genotypes on the treatment of HBV infections require further studies.
Advantages of larval control for African malaria vectors: Low mobility and behavioural responsiveness of immature mosquito stages allow high effective coverage (2002)

Larval control strategies against the vectors of malaria in sub-Saharan Africa could be highly effective, complementary to adult control interventions, and should be prioritized for further development, evaluation and implementation as an integral part of Rolling Back Malaria.
Genes and molecular pathways related to radioresistance of oral squamous cell carcinoma cells (2007)

To identify genes associated with radioresistant oral squamous cell carcinoma (OSCC), we compared gene expression signatures between OSCC cell lines exhibiting radioresistance and cells with radiosensitivity after X-ray irradiation in a dose-dependent manner using Affymetrix GeneChip analysis with Human Genome-U133 plus 2.0 GeneChip. The microarray data identified 167 genes that were significantly overexpressed in radioresistant cells after X-ray irradiation. Among the genes identified, 40 were mapped to 3 highly significant genetic networks identified by the Ingenuity Pathway Analysis tool. Gene ontology analysis showed that cancer-related function had the highest significance. The 40 genes included 25 cancer-related genes that formed 1 network and were categorized by function into growth and proliferation, apoptosis, and adhesion. Furthermore, real-time quantitative reverse transcriptase-polymerase chain reaction showed that the mRNA expression levels of the 25 genes were higher in radioresistant cells than in radiosensitive cells in a dose-dependent manner and in a time-dependent manner. Our results suggest that the identified genes help to elucidate the molecular mechanisms of the radioresistance of OSCC and could be radiotherapeutic molecular markers for choosing the appropriate radiotherapy for this disease.