gebhart/patrepeval huggingface dataset:
[Circadian rhythms and depression]. (1985)

The degree to which nature's cycles influence our body is now obvious, owing to the recent progress of chronobiology. It seems thus that the harmonious internal organization of our circadian rhythms depends on the dual influence of the internal clocks as well as the external temporal informations. These endogenous pacemakers, able to spontaneously generate a rhythmicity the period of which is close to 24 hours, could be triggered by environmental informations, such as light/dark or sleep/Wake cycles, on a 24 hours schedule. The disruption of this entrainment could be involved in major affective disorders. This internal or external desynchronisation seems thus to be the central concept of different models for depression. The internal coincidence model suggests that a phase advance of the strong oscillator in reference to the weak oscillator causes depression. An external coincidence model suggests that depression is caused when light/dark cycle or photoperiod provide too little illumination during a critical photosensitive interval which could be located in the second half of the night. At last, a model comparing the biological rhythms of depressed patients and of healthy volunteers during temporal isolation, suggests that the internal clocks of depressed subjects could be temporarily "blind" to environmental time cues involving internal desynchronisation. These emerging findings should open a new therapeutic approach for depression.
Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys (2009)

Natural SIV infection of sooty mangabeys (SMs) is nonprogressive despite chronic virus replication. Strikingly, it is characterized by low levels of immune activation, while pathogenic SIV infection of rhesus macaques (RMs) is associated with chronic immune activation. To elucidate the mechanisms underlying this intriguing phenotype, we used high-density oligonucleotide microarrays to longitudinally assess host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs was consistently associated with a robust innate immune response, including widespread upregulation of IFN-stimulated genes (ISGs) in blood and lymph nodes. While SMs exhibited a rapid resolution of ISG expression and immune activation, both responses were observed chronically in RMs. Systems biology analysis indicated that expression of the lymphocyte inhibitory receptor LAG3, a marker of T cell exhaustion, correlated with immune activation in SIV-infected RMs but not SMs. Our findings suggest that active immune regulatory mechanisms, rather than intrinsically attenuated innate immune responses, underlie the low levels of immune activation characteristic of SMs chronically infected with SIV.
Human Adult CD34 <sup>−</sup> Progenitor Cells Functionally Express the Chemokine Receptors CCR1, CCR4, CCR7, CXCR5, and CCR10 but Not CXCR4 (2005)

The homing and tissue-specific recruitment of bone marrow-derived progenitor cells is a major issue in stem cell research and therapy. Chemokine biology plays a central role in the homing and trafficking of leukocytes. Here we show functional expression of the chemokine receptors CCR1, CCR4, CCR7, CCR10, and CXCR5 on primary isolates of CD34- mesenchymal progenitor cells as well as immortalized mesenchymal stem cell (MSC) lines. Although mRNA expression of CXCR4 was detected in both primary cells and immortalized clones, the receptor was not expressed on the cell surface. On the basis of this expression profile, the MSC could potentially home to secondary lymphatic organs (CCR7, CXCR5), skin (CCR4, CCR10), small intestine (CCR10), and salivary glands (CCR10). To study tissue-specific homing, murine CD34- MSC lines showing concordant chemokine receptor expression were either transiently labeled with CMFDA, or were stably transfected with green fluorescent protein (GFP) expression plasmids. The MSC were then injected into syngeneic healthy mice, and the distribution of the cells determined. The injected cells efficiently homed to spleen, thymus, and lymph nodes. In addition, cells were found in the mucosa of the small intestine, skin, and salivary gland. No significant recruitment to bone marrow, liver, or kidney was seen. Chemokine biology may play an important role in the homeostasis and potentially tissue recruitment of early adult progenitor cells.
Cell-based assays suggest role for RAB11FIP1 in cell cycle and apoptosis (2008)

AACR Annual Meeting-- Apr 12-16, 2008; San Diego, CA

1847 

RAB11FIP1 is one of several potential oncogenes located in the chromosome 8p11 amplicon which is amplified in 10-15% of human breast cancers (1, 2). It is over-expressed in a panel of breast cancer cell lines but not in MCF10A, a non-tumorigenic human breast epithelial cell line. However, its functions and mechanisms of action are not well characterized. We knocked down RAB11FIP1 with siRNA in a panel of cancer cell lines and observed significantly reduced cell viability. Data from cell-based assays suggest that this reduction in cell viability is caused by 2 mechanisms: increased apoptosis and cell cycle arrest at G2. Increased apoptosis was demonstrated by increased activation of Caspase 3, FOXO3a, PARP cleavage and nuclear condensation across a panel of breast and colon cancer cell lines. Knockdown of RAB11FIP1 also made cells more susceptible to SAHA-induced apoptosis, requiring a lower dose than wild-type cells. In addition, we observed increased activation of p53 and p21 in cells where RAB11FIP1 was knocked down, resulting in G2 arrest. Treatment with SAHA enhanced the p53 and p21 activation in a dose-dependent manner. While wild-type p53 was required for cell cycle arrest induced by RAB11FIP1 knock-down, it was not required for apoptosis induced by RAB11FIP1 knock-down, although presence of wild-type p53 enhanced the apoptotic response. In this paper, we will describe the pathways modulated by RAB11FIP1 and provide evidence supporting its candidacy as an oncogene. References: 1. Yang, Z. Q., Streicher, K. L., Ray, M. E., Abrams, J., and Ethier, S. P. Multiple interacting oncogenes on the 8p11-p12 amplicon in human breast cancer. Cancer Res, 66: 11632-11643, 2006. 2. Garcia, M. J., Pole, J. C., Chin, S. F., Teschendorff, A., Naderi, A., Ozdag, H., Vias, M., Kranjac, T., Subkhankulova, T., Paish, C., Ellis, I., Brenton, J. D., Edwards, P. A., and Caldas, C. A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene, 24: 5235-5245, 2005.
Serum biomarkers in Acute Respiratory Distress Syndrome an ailing prognosticator (2005)

The use of biomarkers in medicine lies in their ability to detect disease and support diagnostic and therapeutic decisions. New research and novel understanding of the molecular basis of the disease reveals an abundance of exciting new biomarkers who present a promise for use in the everyday clinical practice. The past fifteen years have seen the emergence of numerous clinical applications of several new molecules as biologic markers in the research field relevant to acute respiratory distress syndrome (translational research). The scope of this review is to summarize the current state of knowledge about serum biomarkers in acute lung injury and acute respiratory distress syndrome and their potential value as prognostic tools and present some of the future perspectives and challenges.
Aircraft Attitude, Position, and Velocity Determination Using Sensor Fusion (2008)

Inertial Navigation Systems (INS) that have the level of precision needed for Unmanned Aerial Vehicles (UAV) can easily cost more than the vehicle itself; drastically increasing payload weight and power consumption are driving a need for a low cost solution. This can be achieved through the use of sensor fusion techniques on low cost accelerometers and gyroscopes fused with Global Positioning System (GPS) data. In this paper, existing GPS and Inertial Measurement Unit (IMU) flight data is fused with the use of an Extended Kalman filter to better estimate the aircraft attitude, velocity, and position eliminating the need for the high cost attitude sensors. Two sensor fusion methods were implemented and discussed showing that an improvement of position, velocity, and attitude can be achieved using low-cost sensors. The first method utilized the GPS to estimate attitude parameters, which were then in turn used to correct INS attitude values. With this method, improved attitude values were obtained without the calculation of the full INS state; the INS position and velocity are not required, reducing the computational load. The second method uses only the GPS and INS position and velocity to correct for the errors in full state of the INS.
The natural history of adrenal function in autoimmune patients with adrenal autoantibodies (1988)

Adrenal autoantibodies (AA) were found in 23 of 2571 (0.9%) patients with organ-specific autoimmune diseases, in one of 632 first-degree relatives of insulin-dependent diabetic patients, and in none of 375 normal controls. In AA-positive subjects the prevalence of human leucocyte antigens (HLA)-A1, -B8 and -DR3 was significantly higher with respect to the general population. Two groups were followed (15 subjects persistently positive for AA and 51 negative subjects) for a mean period of 3.2 years. Yearly tests were made for AA and adrenal function. Of the 15 subjects persistently positive for AA, six developed Addison's disease after a period varying from 6 months to 10 years. Of the 51 subjects initially negative, two became positive during follow-up, and one of these developed Addison's disease 15 months later. In contrast, all the remaining 49 persistently negative subjects maintained normal adrenal function tests. Overall, of the 17 positive subjects, seven (41%) developed Addison's disease, three (18%) showed various degrees of subclinical adrenocortical failure and the remaining seven maintained normal glandular function. In the positive patients the yearly incidence of detriment in adrenal function was 19%. Patients who developed Addison's disease showed significant association with HLA-B8 phenotype. The development from normal adrenocortical function to overt Addison's disease seemed to progress through four distinct stages of functional impairment: increased plasma renin activity with normal/low aldosterone (stage 1), low cortisol response after i.v. administration of ACTH (stage 2), increased ACTH (stage 3), and low basal cortisol (stage 4).(ABSTRACT TRUNCATED AT 250 WORDS)
Degrees of freedom. (1940)

The article by Walker, H. W. Degrees of Freedom. Journal of Educational Psychology. 31(4) (1940) 253-269, was transcribed from the original by Chris Olsen, George Washington High School, Cedar Rapids, Iowa. Chris has made every attempt to reproduce the look and feel of the article as well as the article itself, and did not attempt in any way to update the symbols to more modern notation. Three typographical errors were found in the paper. These errors are noted in the paragraphs below. The article, except for pagination and placement of diagrams, is as it originally appears. The transcribed pages are not numbered to avoid confusion with pagination in the original article.
Expert object recognition in video (2005)

A recent computer vision technique for object classification in still images is the biologically-inspired Expert Object Recognition (EOR). This thesis adapts and extends the EOR approach for use with segmented video data. Properties of this data, such as segmentation masks and the visibility of an object over multiple frames, are exploited to decrease human supervision and increase accuracy. Several types of runtime learning are facilitated: class-level learning in which object types that are not included in the training set are given artificial classes; viewpoint-level learning in which novel views of training objects are associated with existing classes; and instance-level learning of images that are somewhat similar to training images. The architecture of EOR, consisting of feature extraction, clustering, and cluster-specific principal component analysis, is retained. However, the K-means clustering algorithm used in EOR is replaced in this system by an augmented version of Fuzzy K-means. This algorithm is incrementally run over the lifetime of the system, and automatically determines an appropriate number of partitions based on the data in memory and on a system parameter. In addition, the edge and line-based feature extraction of EOR is replaced with a global application of the principal component analysis, which increases accuracy when used with segmented video data. Classification output for the system consists of a multi-class hypothesis for each tracked object, from which a single-class "hard" hypothesis may be determined. The system, named VEOR (video expert object recognition), is designed for and tested with noisy, automatically segmented real-world data, consisting of both videos and still images of vehicle (car, pickup truck, and van) profiles.
Physiological characterization of the yeast metallothionein (<i>CUP1</i>) promoter, and consequences of overexpressing its transcriptional activator, <i>ACE1</i> (1994)

Using the anticoagulant, hirudin, from the leech Hirudo medicinalis as a secreted reporter protein, the influence of physiological parameters on activity and regulation of the yeast (Saccharomyces cerevisiae) metallothionein (CUP1) promoter was studied. Induction of CUP1-directed hirudin expression from 2 mu-based vectors was possible at any time point during diauxic batch growth, even in cells approaching stationary phase. The highest titers of hirudin were obtained when the CUP1 promoter was activated immediately following inoculation of the cultures. If such a pseudo-constitutive fermentation strategy was adopted, the promoter was superior to an optimized variant (GAPFL) of the strong, constitutive GAPDH promoter. This superiority was primarily due to the relative independence of CUP1 promoter activity of the physiological status of host cells: whilst the maximal strength of the CUP1 and GAPFL promoters was comparable, CUP1-directed hirudin expression was high in all phases of diauxic batch growth, whereas hirudin production from the GAPFL promoter declined in post-diauxic cultures. High activity of the CUP1 promoter was observed on both a fermentable (glucose) and a non-fermentable (ethanol) carbon source. Hirudin expression could be adjusted to different levels by varying the amount of inducer (cupric sulphate) added to cultures. The copper concentrations required for maximal promoter induction had no negative effects on host growth and interfered with neither hirudin secretion nor with the biological activity of the peptide. Overexpression of the transcriptional activator, ACE1, resulted in increased levels of hirudin mRNA. Hirudin titers increased in parallel to mRNA concentrations in cultures grown in the presence of low concentrations of copper. In contrast, at high copper doses, elevated levels of the ACE1 protein resulted in inferior hirudin production. Cells overexpressing ACE1 while harbouring a CUP1-drived hirudin expression cassette showed slow growth and poor plasmid maintenance. It was tested whether this might be the result of a block in the secretory pathway; however, measurements of intracellular hirudin did not support this hypothesis. The data rather indicated that hirudin production was limited by a metabolic constraint downstream of transcription but upstream of the secretory pathway.
Electrodeposition of Cu-doped ZnO nanowire arrays and heterojunction formation with p-GaN for color tunable light emitting diode applications (2011)

Copper-doped zinc oxide (ZnO:Cu) nanowires (NWs) were electrochemically deposited at low temperature on fluor-doped tin oxide (FTO) substrates. The electrochemical behavior of the Cu–Zn system for Cu-doped ZnO electrodeposition was studied and the electrochemical reaction mechanism is discussed. The synthesized ZnO arrayed layers were investigated by using SEM, XRD, EDX, photoluminescence and Raman techniques. X-ray diffraction analysis demonstrates a decrease in the lattice parameters of Cu-doped ZnO NWs. Structural analyses show that the nanomaterial is of hexagonal structure with the Cu incorporated in ZnO NWs probably by substituting zinc in the host lattice. Photoluminescence studies on pure and Cu-doped ZnO NWs shows that the near band edge emission is red-shifted by about 5 or 12 nm depending on Cu(II) concentration in the electrolytic bath solution (3 or 6 μmol l−1). Cu-doped ZnO NWs have been also epitaxially grown on Mg doped p-GaN single-crystalline layers and the (ZnO:Cu NWs)/(p-GaN:Mg) heterojunction has been used to fabricate a light-emitting diode (LED) structure. The emission was red-shifted to the visible violet spectral region compared to pure ZnO. The present work demonstrates the ability of electrodeposition to produce high quality ZnO nanowires with tailored optical properties by doping. The obtained results are of great importance for further studies on bandgap engineering of ZnO, for color-tunable LED applications and for quantum well preparation.
Reaction of human UMP‐CMP kinase with natural and analog substrates (2003)

UMP-CMP kinase catalyses an important step in the phosphorylation of UTP, CTP and dCTP. It is also involved in the necessary phosphorylation by cellular kinases of nucleoside analogs used in antiviral therapies. The reactivity of human UMP-CMP kinase towards natural substrates and nucleotide analogs was reexamined. The expression of the recombinant enzyme and conditions for stability of the enzyme were improved. Substrate inhibition was observed for UMP and CMP at concentrations higher than 0.2 mm, but not for dCMP. The antiviral analog l-3TCMP was found to be an efficient substrate phosphorylated into l-3TCDP by human UMP-CMP kinase. However, in the reverse reaction, the enzyme did not catalyse the addition of the third phosphate to l-3TCDP, which was rather an inhibitor. By molecular modelling, l-3TCMP was built in the active site of the enzyme from Dictyostelium. Human UMP-CMP kinase has a relaxed enantiospecificity for the nucleoside monophosphate acceptor site, but it is restricted to d-nucleotides at the donor site.
A Nonparametric Valley-Seeking Technique for Cluster Analysis (1972)

The problem of clustering multivariate observations is viewed as the replacement of a set of vectors with a set of labels and representative vectors. A general criterion for clustering is derived as a measure of representation error. Some special cases are derived by simplifying the general criterion. A general algorithm for finding the optimum classification with respect to a given criterion is derived. For a particular case, the algorithm reduces to a repeated application of a straightforward decision rule which behaves as a valley-seeking technique. Asymptotic properties of the procedure are developed. Numerical examples are presented for the finite sample case.
Novel pulse generator architecture dedicated to low data rate UWB systems (2005)

This paper introduces a new transmitter architecture for UWB impulse radio communication dedicated to 3.1-5.1GHz band. The latter is developed for applications targeting data rates up to 1Mbps, associated with location and fine positioning. First, through a windowed cosine pulse model, power and spectral analysis of generated pulses are presented. Then, based on previous results, a pulse generator architecture is proposed and its design specifications are studied more in detail.
Content-based video retrieval using mosaic images (2003)

Content-based video retrieval is one of the most active multimedia research issues. We propose a system for retrieving video data by means of mosaic images. Mosaicing is a technique of joining/merging frames of a shot into one blended image. The resulting mosaic image can convey three primitive features in videos, that is, background, (moving) objects, and camera work such as pan, tilt and zoom. Thanks to this capability, the user can retrieve video databases effectively by specifying queries encompassing the condition of these three types of video features.
Microfabrication of Three-Dimensional Structures in Polymer and Glass by Femtosecond Pulses (2002)

We report three-dimensional laser microfabrication, which enables microstructuring of materials on the scale of 0.2-1 micrometers. The two different types of microfabrication demonstrated and discussed in this work are based on holographic recording, and light-induced damage in transparent dielectric materials. Both techniques use nonlinear optical excitation of materials by ultrashort laser pulses (duration < 1 ps).
Simulation and Optimization of Power DMOS Transistors Parameters (2006)

At present power DMOS transistors are regarded as one of the most prospective components for many power-saving devices. When developing power DMOS transistors, which parameters are analogs of IRL640, "transistor factory" of RPC "integral" used the skills of physical and layout simulation and design of low-power LSI having N-channel MOS transistor structures. Based on this approach and using the developed original software, conducted was optimization of parameters of solid-state structure of power DMOS transistors of KP728E1 type. In particular, minimized were the resistance values between the drain and source areas in the transistor "open" state, output and pass-by capacitances of cell transistor structure when maintaining other parameters at the set level. Given are resistive and capacitance models of a DMOS transistor. Resistance of a conductive channel in an elementary cell of a DMOS transistor was calculated as the sum of capacitances of a solid-state structure, including herein the induced channel of a horizontal N-MOS transistor, and the cell's capacitances are optimized taking into account SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thickness in different parts of the structure
Role of Hyaluronan and Reactive Oxygen Species in Tissue Kallikrein-mediated Epidermal Growth Factor Receptor Activation in Human Airways (2004)

In human airways, oxidative stress-induced submucosal gland cell hypertrophy and hyperplasia, histological features of chronic bronchitis, have been linked to epidermal growth factor receptor (EGFR) activation. To explore mechanisms of oxidative stress-induced EGFR activation and signaling, primary cultures of human tracheal submucosal gland (SMG) cells were used to assess EGFR ligand release, EGFR phosphorylation, p44/42 MAPK phosphorylation, and mucin 5AC synthesis in response to reactive oxygen species generated by xanthine/xanthine oxidase (X/XO). Exposure to X/XO increased release of epidermal growth factor (EGF) from these cells, thereby activating EGFR, phosphorylating MAPK, and increasing mucin 5AC production. The importance of EGF was confirmed by transfection of small interfering RNA inhibiting pro-EGF production, which resulted in inhibition of EGFR and MAPK phosphorylation despite X/XO exposure. Blocking signaling by using specific protease inhibitors showed that tissue kallikrein (TK) processed pro-EGF in response to X/XO. Airway TK is bound and inactivated by luminal hyaluronan (HA), and treatment of submucosal gland cells with X/XO induced HA depolymerization and TK activation. These events were blocked by reactive oxygen species scavengers and addition of exogenous excess HA and TK inhibitors. Thus, HA plays a crucial role in regulating airway TK activity and thereby TK-mediated release of active EGF from human SMG cells. Sustained HA depolymerization is expected to cause TK activation, EGF release, and EGFR signaling and to lead to SMG cell hypertrophy and hyperplasia as well as mucus hypersecretion with subsequent airflow obstruction.