gebhart/patrepeval huggingface dataset:
Reconfigurable all-optical crossconnect node using synthesized fiber Bragg gratings for both demultiplexing and switching (1998)

We introduce an optical crossconnect architecture using all-fiber technology. The key components are synthesized fiber Bragg gratings written using a position weighting technique. The fiber Bragg gratings are used to perform the required combination of wavelength filtering and space routing The grating synthesis allows optimization of all important grating characteristics: spectral flatness, dispersion, edges roll-off, and side lobes.
High reproducibility of large‐gel two‐dimensional electrophoresis (2004)

Two-dimensional gel electrophoresis (2-DE) facilitates the separation of thousands of proteins from highly complex protein mixtures and has become a central method in proteomics in recent years. In the present study, we examined the technical variability of large 2-DE gels with respect to sample preparation, electrophoresis procedure, data acquisition, and biological variation by analyzing a disease (Huntington's disease) and control state with a commercially available software package, PROTEOMWEAVER trade mark. Scatter plots and correlation coefficients were obtained to quantify both technical and biological variation. Even 2-DE gels run separately in both dimensions yielded correlation coefficients around 0.88 and deviations from the mean close to 20% for low-intensity spots. This indicates a high technical reproducibility of the 2-DE procedure developed in our laboratory. Variability within a biological condition was low and comparable to technical variation (at least 0.87). Two-dimensional (2-D) gels obtained from samples of different biological conditions (health vs. disease) achieved a variability similar to intracondition and technical variability. These findings highlight the importance of multiple gel and spot-by-spot comparisons to identify biological significant changes. Minor errors introduced by technical and biological variation allow a comparison of all gels within a study which facilitates the tackling of complex biological problems.
Identification of differentially expressed genes representing dendritic cell precursors and their progeny (2003)

The development of dendritic cells (DCs) from hematopoietic progenitors is not well understood. Using a spleen-derived long-term culture (LTC) system, it has been possible to continuously generate DCs from progenitors maintained in culture. The nonadherent LTC-DC population is composed of 2 major subsets. These are the small LTC-DC or DC precursors and their progeny, the large LTC-DCs that phenotypically resemble immature DCs. In this study, subtracted cDNA libraries were generated containing sequences differentially expressed in small or large LTC-DCs. Differential screening was then used on plated library clones to select genes expressed in either the small or the large cell population. Real-time polymerase chain reaction (PCR) has been used to verify the selection procedure for several genes of particular interest. Known genes isolated from subtracted libraries were related to stages in DC development and supported previous findings regarding the function of small and large LTC-DCs. Large LTC-DCs expressed a number of immunologically important genes encoding CD86, CCR1, osteopontin, and lysozyme. Small LTC-DCs resembled progenitor DCs expressing genes related to the organization of the cytoskeleton, the regulation of antigen processing, and a number of mitochondrial and ribosomal proteins. Novel transcripts were isolated from small and large LTC-DC-subtracted libraries that could encode novel proteins important in DC development. This study describes changes in gene expression related to the development of CD11c+CD11b+ major histocompatibility complex 2 low (MHC2lo) CD8alpha- DCs from precursors in a stroma-dependent culture system in the absence of exogenous cytokines.
Comprehensive Analysis of Conditioned Media from Ovarian Cancer Cell Lines Identifies Novel Candidate Markers of Epithelial Ovarian Cancer (2009)

Ovarian cancer remains a deadly threat to women as the disease is often diagnosed in the late stages when the chance of survival is low. There are no good biomarkers available for early detection and only a few markers have shown clinical utility for prognosis, response to therapy and disease recurrence. We mined conditioned media of four ovarian cancer cell lines (HTB75, TOV-112D, TOV-21G and RMUG-S) by two-dimensional liquid chromatography-mass spectrometry. Each cell line represented one of the major histological types of epithelial ovarian cancer. We identified 2039 proteins from which 228 were extracellular and 192 were plasma membrane proteins. Within the latter list, we identified several known markers of ovarian cancer including three that are well established, namely, CA-125, HE4, and KLK6. The list of 420 extracellular and membrane proteins was cross-referenced with the proteome of ascites fluid to generate a shorter list of 51 potential biomarker candidates. According to Ingenuity Pathway Analysis, two of the top 10 diseases associated with the list of 51 proteins were cancer and reproductive diseases. We selected nine proteins for preliminary validation using 20 serum samples from healthy women and 10 from women with ovarian cancer. Of the nine proteins, clusterin (increase) and IGFBP6 (decrease) showed significant differences between women with or without ovarian cancer. We conclude that in-depth proteomic analysis of cell culture supernatants of ovarian cancer cell lines can identify potential ovarian cancer biomarkers that are worth further clinical validation.
Towards Better Availability and Accountability for IoT Updates by Means of a Blockchain (2017)

Building the Internet of Things requires deploying a huge number of objects with full or limited connectivity to the Internet. Given that these objects are exposed to attackers and generally not secured-by-design, it is essential to be able to update them, to patch their vulnerabilities and to prevent hackers from enrolling them into botnets. Ideally, the update infrastructure should implement the CIA triad properties, i.e., confidentiality, integrity and availability. In this work, we investigate how the use of a blockchain infrastructure can meet these requirements, with a focus on availability. In addition, we propose a peer-to-peer mechanism, to spread updates between objects that have limited access to the Internet. Finally, we give an overview of our ongoing prototype implementation.
MBD3L1 Is a Transcriptional Repressor That Interacts with Methyl-CpG-binding Protein 2 (MBD2) and Components of the NuRD Complex (2004)

Methyl-CpG-binding domain proteins 2 and 3 (MBD2 and MBD3) are transcriptional repressors that contain methyl-CpG binding domains and are components of a CpG-methylated DNA binding complex named MeCP1. Methyl-CpG-binding protein 3-like 1 (MBD3L1) is a protein with substantial homology to MBD2 and MBD3, but it lacks the methyl-CpG binding domain. MBD3L1 interacts with MBD2 and MBD3 in vitro and in yeast two-hybrid assays. Gel shift experiments with a CpG-methylated DNA probe indicate that recombinant MBD3L1 can supershift an MBD2-methylated DNA complex. In vivo, MBD3L1 associates with and colocalizes with MBD2 but not with MBD3 and is recruited to 5-methylcytosine-rich pericentromeric heterochromatin in mouse cells. In glutathione S-transferase pull-down assays MBD3L1 is found associated with several known components of the MeCP1.NuRD complex, including HDAC1, HDAC2, MTA2, MBD2, RbAp46, and RbAp48, but MBD3 is not found in the MBD3L1-bound fraction. MBD3L1 enhances transcriptional repression of methylated DNA by MBD2. The data are consistent with a role of MBD3L1 as a methylation-dependent transcriptional repressor that may interchange with MBD3 as an MBD2-interacting component of the NuRD complex. MBD3L1 knockout mice were created and were found to be viable and fertile, indicating that MBD3L1 may not be essential or there is functional redundancy (through MBD3) in this pathway. Overall, this study reveals additional complexities in the mechanisms of transcriptional repression by the MBD family proteins.
Bubbling reefs in the Kattegat: submarine landscapes of carbonate-cemented rocks support a diverse ecosystem at methane seeps (1992)

Methane seeps in shallow waters In the northern Kattegat off the Danish coast form spectacular submarine landscapesthe 'bubbling reefs'due to carbonate-cemented sandstone structures which are colonized by brightly coloured animals and plants. These structures may be 100 m2 in area and consist of pavements, complex formations of overlying slab-type layers, and pillars up to 4 m high. The carbonate cement (high-magnesium calcite, dolomite or aragonite) is 13C-depleted, indicating that it originated as a result of microbial methane oxidation. It is believed that the cementation occurred in the subsurface and that the rocks were exposed by subsequent erosion of the surrounding unconsolidated sediment. The formations are interspersed with gas vents that intermittently release gas, primarily methane, at up to 25 1 h-' The methane most likely originated from the microbial decomposition of plant material deposited during the Eemian and early Weichselian periods, i.e. l00 000 to 125 000 years B.P. Aerobic methane oxidation in the sediment was restricted Lo the upper 4 cm in muddy sand and to the upper 13 cm In coarse sand. Maximum aerobic methane oxidation rates ranged from 4.8 to 45.6 pm01 dm-3 d". The rock surfaces and epifauna around the seeps were also sites of methane-oxidizing activity. Integrated sulphate reduction rates for the upper 10 cm of muddy sand gave 4.2 to 26.6 mm01 m-2 d-' These rates are higher than those previously reported from similar water depths in the Kattegat but did not relate to the sediment methane content. Since gas venting occurs over several km2 of the sea floor in the Kattegat it is likely to make a significant local contribution to the cycling of elements in the sediment and the water column. The rocks support a diverse ecosystem ranging from bacteria to macroalgae and anthozoans. Many animals live within the rocks in holes bored by sponges, polychaetes and bivalves. Stable carbon isotope composition (6'") of tissues of invertebrates from the rocks were in the range -17 to -24 'A, indicating that methane-derived carbon makes little direct contribution to their nutrition. Within the sediments surrounding the seeps there is a poor metazoan fauna, in terms of abundance, diversity and biomass. This may be a result of toxicity due to hydrogen sulphide input from the gas.
A new circularly polarized monopole antenna for 60 GHz communications (2014)

This paper presents a novel broadband unidirectional circularly polarized (CP) monopole antenna. The proposed antenna, which is based on traveling wave excitation, is compact in size and simple in structure. It consists of a ground plane, a probe, and an L-shaped strip. A 4×4-element array on low temperature cofired ceramic (LTCC) for the 60 GHz band is also presented. Simulation results of the antenna array show a 3-dB axial ratio bandwidth of 30% (51–69 GHz), which is within its −15-dB impedance bandwidth. Meanwhile, the 3-dB gain bandwidth is 27% (51.5–67.5 GHz) with a peak gain of 16.2 dBi.
Schisandrin B down‐regulated lnc<scp>RNA BCYRN</scp>1 expression of airway smooth muscle cells by improving miR‐150 expression to inhibit the proliferation and migration of <scp>ASMC</scp> in asthmatic rats (2017)

Schisandrin B increased miR-150 expression and decreased BCYRN1, and BCYRN1 expression was inhibited by miR-150, which indicated that Schisandrin B could regulate BCYRN1 through miR-150.
Mutations at the Darkener of apricot locus modulate transcript levels of copia and copia-induced mutations in Drosophila melanogaster. (1993)

Mutations of the Doa locus of Drosophila melanogaster darken the eye color of the copia-induced white(apricot) (wa) allele and increase the accumulation of white promoter-initiated transcripts encoding functional mRNA. We show here that quantities of transcripts initiated in both long terminal repeats (LTRs) of the specific wa-copia element are increased, and those initiating in the 5' LTR of the element are structurally altered, yielding a slightly shortened transcript. Accumulation of host-initiated transcripts of a copia-induced mutation within the achaete-scute complex, Hairy-wing Ua (HwUa), are reduced by Doa mutations. Finally, we show that homozygosity for Doa mutations increases the accumulation of copia transcripts from the population of elements in the genome. These results suggest that Doa modulates the severity of copia-induced mutations while functioning as a dosage-sensitive modulator of copia transcription.
A Comparison of postposed subjects in English and Italian (1999)

L'A. examine les contraintes discursives sur l'utilisation d'un certain nombre de constructions anglaises et italiennes, dans lesquelles le sujet logique apparait en position postverbale, laissant la position preverbale vide ou occupee par un element expletif. Il montre que toutes ces constructions exigent que le SN postpose represente une entite qui soit, en quelque sorte, non familiere, bien que le type de non familiarite exige differe selon les types de phrase. Les phrases presentatives avec there en anglais et les phrases avec ci en italien et la postposition du sujet sont sensibles au statut discursif du constituant postpose (information nouvelle/ancienne pour le discours). Les phrases existentielles avec there en anglais, par contre, sont sensibles au statut de ce constituant pour l'auditeur (information nouvelle/ancienne pour l'auditeur)
Photodynamic Imaging of a Rat Pancreatic Cancer with Pheophorbide a (1996)

Laser-induced fluorescence of pheophorbide a (Ph-a) was used for in vitro photodynamic imaging (PDI) of a rat pancreatic acinar tumor. A 400 nm excitation induced a 470 nm autofluorescence and a 678 nm dye fluorescence in tumors and their surrounding pancreas 24 h after a 9 mg kg-1 body weight Ph-a intravenous administration. With lower intensities in these blood-rich tumors than in pancreas, Ph-a fluorescence signals are unable to provide tumor images. A dimensionless function (the ratio of Ph-a fluorescence by autofluorescence, called Rt for the tumor and Rp for the pancreas) was used for fluorescence contrast calculation (C = Rt/Rp) between six tumors and their paired pancreas. Among five available laser excitation wave-lengths, only the 355 nm excitation gave a distinctive contrast (C = 1.5). The PDI of six intrapancreatic tumors and their intraperitoneal metastasis and of two control normal pancreas was thus performed ex vivo using a 355 nm excitation source delivered by a tripled Nd:YAG laser and a charged-coupled device camera. Fluorescence images were recorded at 680 nm (dye), 640 nm (background) and 470 nm (autofluorescence) through three corresponding 10 nm width bandpass filters. Computed division for each pixel of Ph-a fluorescence values by autofluorescence generated false color image. In this way, contrasted tumor images were obtained. But in five out of six animals false-positive images were present due to an autofluorescence decrease in some normal pancreatic areas. A 470 nm autofluorescence imaging on the same tumors gave in all cases false-positive image and false-negative in half of the cases. These observations suggest that autofluorescence alone is unable to achieve accurate PDI of pancreatic carcinoma and that using Ph-a as a PDI dye needs strong improvements.
Non-conservative homologous recombination in human B lymphocytes is promoted by activation-induced cytidine deaminase and transcription (2008)

During secondary immunoglobulin (Ig) diversification in vertebrates, the sequence of the variable region of Ig genes may be altered by templated or non-templated mechanisms. In both cases, cytidine deamination by activation-induced cytidine deaminase (AID) in the transcribed Ig loci leads to DNA lesions, which are repaired by conservative homologous recombination (HR) during Ig gene conversion, or by non-templated mutagenesis during somatic hypermutation. The molecular basis for the differential use of these two pathways in different species is unclear. While experimental ablation of HR in avian cells performing Ig gene conversion may promote a switch to somatic hypermutation, the activity of HR processes in intrinsically hypermutating mammalian cells has not been measured to date. Employing a functional HR assay in human germinal centre like B cell lines, we detect elevated HR activity that can be enhanced by transcription and AID. Products of such recombination events mostly arise through non-conservative HR pathways, while the activity of conservative HR is low to absent. Our results identify non-conservative HR as a novel DNA transaction pathway promoted by AID and suggest that somatic hypermutation in germinal centre B cells may be based on a physiological suppression of conservative HR.
Occurrence of highly fluoroquinolone-resistant and methicillin-resistant<i>Staphylococcus aureus</i>in domestic animals (2007)

We describe phenotypic and genotypic analyses carried out on multidrug-resistant Staphylococcus aureus isolated from domestic animals. The sequence type ST239 methicillin-resistant Staphylococcus aureus isolated from dogs were highly resistant to fluoroquinolones, and new combinations of GyrA and GrlA mutations were identified. These findings are consistent with a role for animal carriage in the dissemination of important human pathogens in the community.
Extended state observer based sliding mode control of electronic throttle valve (2014)

In order to improve the control precision of electronic throttle, the extended state observer, which is used to estimate the change of throttle opening, is designed based on nonlinear model of electronic throttle. In addition, the sliding mode controller has been built through the Lyapunov theory based on the throttle error and differential of throttle error. Finally, the simulation is conducted and the results show that the proposed controller can track the desired signal better than the approach of literature [1] is used.
Interferon therapy of metastatic renal cell cancer (1988)

There is no curative therapy for metastatic or recurrent renal cell carcinoma (RCC). Almost three-quarters of such patients die of their malignancy in 1 year and less than 5% of such patients are alive at 3 years. Few patients respond to hormonal therapy or chemotherapy, and when responses occur, they are usually brief and partial with little impact on survival. Interferon therapy in metastatic RCC has been associated with response rates of approximately 15-20%, and tumor regression has been demonstrated in patients treated with both partially purified and, more recently, recombinant interferon. Analysis of published trials shows no clear dose-response relationship; however, the highest therapeutic index appears associated with a daily dosage of 5-10 million units. The time to response is variable and may occasionally be prolonged; however, some patients have durations of response exceeding 12 months. Although nephrectomy may be associated with higher response rates, review of available data indicates that nephrectomy has frequently been an eligibility criteria, and indeed there are adequate descriptions of responses in patients that have not undergone this procedure. Patients with pulmonary metastases have the highest response rate. Recently, laboratory and clinical investigations of interferons and several chemotherapeutic agents, notably vinblastine, suggest synergy, but further data is needed to confirm these findings. The role of interferon therapy in improving survival is unknown. There is little doubt, however, that symptomatic patients who respond to interferon therapy may show improvement in their quality of life and prolongation of survival.
Sleep Matters: Why Getting Toddlers to Sleep, and to Stay Asleep, Is Important (2009)

3. This study is part of the broader CIHR-funded Parenting Matters Program headed by Dr. Reid. Bringing research to practice, this program aims to help parents of young children deal effectively with sleep and discipline problems - the two most common early childhood problems, both of which can have a lasting impact on child development. Although the link between sleep and behaviour problems has been wellestablished by past research, few studies have attempted to identify other factors, such as parenting styles, that might account for this link. Nor have they developed models to explain how such factors might contribute to these problems. The present study set out to fill these research gaps using data on three separate cohorts of 2-3 year old children from Canada’s National Longitudinal Study of Children and Youth (NLSCY). From 1994 onwards, this survey has collected information every two years from the mother (or another adult close to the child) on a wide range of aspects about herself, her family and her child. The questions used in this analysis relate to children’s sleep difficulties (specifically night waking and bedtime resistance), emotional and behaviour problems (anxiety, hyperactivity, and aggression) - and characteristics of the family (family functioning, income, marital status) and parent (parenting, depressive symptoms). In all three samples, young children who had difficulty getting to sleep or staying asleep were more likely to suffer from emotional and behavioural problems. The regression analyses found that this relationship remained even after other well-established risk factors were taken into account. In fact, among young children, sleep problems were as strongly associated with anxiety, hyperactivity and aggression as parental depression. In other words, sleep has a unique effect on young children’s emotional and behavioural functioning.
Design of a Multifunctional Compliant Instrument for Minimally Invasive Surgery (2005)

A new multifunctional compliant instrument has been designed for use in minimally invasive surgery. The instrument combines scissors and forceps into a single multifunctional device. The main advantage of using multifunctional instruments for minimally invasive surgery is that instrument exchanges can be reduced, thus reducing procedure time and risk of inadvertent tissue injury during instrument exchanges. In this paper, the length, width, and thickness of the multifunctional compliant mechanism tool tip is optimized to maximize the jaw opening and the grasping force. The optimized design is then modeled to simulate the stresses encountered in the scissors mode. A 5.0 mm diameter stainless steel prototype is fabricated using electro-discharge machining and is shown to grasp and cut successfully.
Prevention of Tendon Adhesions by ERK2 Small Interfering RNAs (2013)

Tendon adhesions are one of the most concerning complications after surgical repair of flexor tendon injury. Extracellular signal-regulated kinase (ERK) 2 plays crucial roles in fibroblast proliferation and collagen expression which contributes to the formation of tendon adhesions after flexor tendon surgery. Using a chicken model, we have examined the effects of a small interfering RNA (siRNA) targeting ERK2 delivered by a lentiviral system on tendon adhesion formation with an adhesion scoring system, histological assessment, and biomechanical evaluation. It was found that ERK2 siRNA effectively suppressed the increase of fibroblasts and the formation of tendon adhesions (p < 0.05 compared with the control group). Moreover, no statistically significant reduction in breaking force was detected between the ERK2 siRNA group and the control group. These results show that the lentiviral-mediated siRNA system is effective in preventing tendon adhesion formation but not to tendon healing, and may be used for tendon repair after confirmation and improvement by future detailed studies.