gebhart/patrepeval huggingface dataset:
Downregulation of Sec23A Protein by miRNA-375 in Prostate Carcinoma (2011)

Prostate carcinoma (CaP) is a leading cause of cancer-related death in men. We have previously determined the microRNA (miRNA) profile of primary CaP in comparison with nontumor prostate tissue. miRNAs are small, noncoding RNAs that inhibit protein synthesis on a posttranscriptional level by binding to the 3'-untranslated region (3'-UTR) of their target genes. In primary CaP tissue, we have previously found by miRNA sequencing that miR-375 and miR-200c were upregulated 9.1- and 4.5-fold, respectively. A computational analysis predicted the 3'-UTR of the SEC23A gene as a potential target for both miR-375 and miR-200c. Here, we show that the 3'-UTR of SEC23A mRNA is indeed a target for miR-375 and miR-200c and that both miRNAs downregulate Sec23A protein expression when ectopically expressed in human 293T cells. In primary samples of CaP, we found a direct correlation between reduction of SEC23A mRNA and overexpression of miR-375 but not of miR-200c. The reduced levels of Sec23A protein were inversely correlated to the increased amount of miR-375 in the LNCaP and DU145 CaP cell lines when compared with normal prostate fibroblasts. In primary CaP, we also detected decreased amounts of Sec23A protein when compared with corresponding normal prostate tissue. Ectopically overexpressed Sec23A in LNCaP and DU145 CaP cells significantly reduced the growth properties, indicating that Sec23A might play a role in the induction or growth of prostate carcinoma. Sec23A overexpression reduced cell growth but did not induce apoptosis, whereas inhibition of Sec23A stimulated cell proliferation.
Effects of Culture Medium, Serum Type, and Various Concentrations of Follicle-Stimulating Hormone on Porcine Preantral Follicular Development and Antrum Formation In Vitro1 (2002)

Developing a culture system for preantral follicles has important biotechnological implications due to the potential to produce large number of oocytes for embryo production and transfer. As an initial step toward accomplishing this long-term goal, a study was conducted to determine the effects of culture medium, serum type, and different concentrations of FSH on preantral follicular development in vitro. Specific endpoints included follicular growth rate, antrum formation, recovery rate of cumulus cell-oocyte complexes (COCs) from follicles, and oocyte meiotic competence. Compared with the North Carolina State University medium 23 (NCSU23), preantral follicles cultured in TCM199 medium for 4 days grew faster (P < 0.02). However, more follicles cultured in NCSU23 differentiated to form an antrum than in TCM199 (P < 0.01). For this reason, NCSU23 was chosen to investigate the role of FSH and serum type in regulating preantral follicular growth. Compared with the 0 mIU/ml FSH control, addition of 2 mIU/ml FSH to the medium stimulated follicular growth and antrum formation and suppressed apoptosis of granulosa cells (P < 0.05), supporting the essential role of FSH in preantral follicular growth and development. Another experiment compared fetal calf serum (FCS) with prepubertal gilt serum (PGS) and studied different concentrations of FSH in the culture medium (0.5, 1, and 2 mIU/ml). The best follicular growth rate was obtained with 2 mIU/ml compared with 0.5 or 1 mIU/ml FSH. Compared with PGS, FCS supplementation increased the cumulative percentage of antral follicles and COC recovery rate (P < 0.04). None of the oocytes recovered from any of these experiments reached metaphase II stage after maturation in vitro. In summary, culture medium, serum type, and FSH concentration in the medium interacted to affect follicular growth and antrum formation in vitro. These results suggest that a longer term culture of preantral follicles (>4 days) may be needed to produce oocytes capable of undergoing meiosis in vitro.
Effectiveness and Kinetics of Ferrate as a Disinfectant for Ballast Water (2008)

This study examined whether ferrate could meet the international standards for successful ballast water treatment, including final concentrations of less than 1 CFU/mL of Enterococci, less than 2.5 CFU/mL of Escherichia coli, and less than 1 CFU/100 mL of Vibrio cholerae. Pure cultures of E. coli, Klebsiella pneumoniae, and V. cholerae, and a mixed culture of Enterococcus faecium and E. faecilis were grown in saline solution to simulate ballast water and were treated with dosages of ferrate ranging from 0.25 to 5.0 mg/L. A ferrate dose of 5 mg/L resulted in complete disinfection of all organisms tested, and smaller dosages were also very effective. Tailing was consistently observed, and the Hom's model (1972) appeared to most accurately represent the action of ferrate on these organisms. Salinity and pH did not adversely affect results, and regrowth was not a problem. Ferrate shows good potential as an effective disinfectant in the treatment of ballast water.
Interrogating the Lewis Acidity of Metal Sites in Beta Zeolites with 15N Pyridine Adsorption Coupled with MAS NMR Spectroscopy (2016)

The Lewis acidity of isolated framework metal sites in Beta zeolites was characterized with <sup>15</sup>N isotopically labeled pyridine adsorption coupled with magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy. The <sup>15</sup>N chemical shift of adsorbed pyridine was found to scale with the acid character of both Lewis (Ti, Hf, Zr, Nb, Ta, and Sn) and Brønsted (B, Ga, and Al) acidic heteroatoms. The <sup>15</sup>N chemical shift showed a linear correlation with Mulliken electronegativity of the metal center in the order Ti < Hf < Zr < Nb < Ta < Sn < H<sup>+</sup>. Theoretical calculations using density functional theory (DFT) showed a strong correlation between experimental <sup>15</sup>N chemical shift and the calculated metal-nitrogen bond dissociation energy, and revealed the importance of active site reorganization when determining adsorption strength. The relationships found between <sup>15</sup>N pyridine chemical shift and intrinsic chemical descriptors of metal framework sites complement adsorption equilibrium data and provide a robust method to characterize, and ultimately optimize, metal-reactant binding and activation for Lewis acid zeolites. Direct <sup>15</sup>N MAS NMR detection protocols applied to the Lewis acid-base adducts allowed the differentiation and quantification of framework metal sites in the presence of extraframework oxides, including highly quadrupolar nuclei that are not amenable for quantification with conventional NMR methods.
Very Strong Binding for a Neutral Calix[4]pyrrole Receptor Displaying Positive Allosteric Binding (2017)

The dual-analyte responsive behavior of tetraTTF-calix[4]pyrrole receptor 1 has been shown to complex electron-deficient planar guests in a 2:1 fashion by adopting a so-called 1,3-alternate conformation. However, stronger 1:1 complexes have been demonstrated with tetraalkylammonium halide salts that defer receptor 1 to its cone conformation. Herein, we report the complexation of an electron-deficient planar guest, 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA, 2) that champions the complexation with 1, resulting in a high association constant K<sub>a</sub> = 3 × 10<sup>10</sup> M<sup>-2</sup>. The tetrathiafulvalene (TTF) subunits in the tetraTTF-calix[4]pyrrole receptor 1 present a near perfect shape and electronic complementarity to the NTCDA guest, which was confirmed by X-ray crystal structure analysis, DFT calculations, and electron density surface mapping. Moreover, the complexation of these species results in the formation of a charge transfer complex (2<sub>2</sub>⊂1) as visualized by a readily apparent color change from yellow to brown.
The Role of T Regulatory Cells in Chlamydia trachomatis Genital Infection (2012)

T cell-mediated immune suppression of adaptive immune responses is important for the homeostatic function of tissues. Compelling evidence has found that the normal immune system produces T cells with a specialized function in immune suppression and this type of T cell is called a regulatory T cell (TRC). There are various types of TRCs with suppressive function. The majority of TRCs express the transcription factor called forkhead box p3 or Foxp3, and play a pivotal role in the maintenance of immune tolerance by preventing autoimmunity and rejection of transplanted tissue Recently TRCs have also been implicated in preventing inflammatory diseases. Extensive evidence has shown that TRCs exacerbate and suppress inflammatory responses in various diseases, including the human multiple sclerosis model, experimental autoimmune encephalomyelitis (EAE) TRCs also play major roles in regulating immunity to infections of viral, bacterial or parasitic pathogens. TRCs dampen immune response which control pathogen replication. In many instances, these responses increase pathogen survival. Alternatively, TRCs can also limit collateral tissue damage caused by powerful immune responses directed toward microbes However, tumors and microbes commandeer the immune suppressive properties of TRCs to evade host immunity and cause disease. This is especially prominent at mucosal tissues since they are exposed to a plethora of pathogens. In this review, we will introduce the broad category of TRCs with focus on their phenotype, function and role in maintaining mucosal tissues, especially of the genital tract.
Impact of three-dimensional current flow on accurate TCAD simulation for trench-gate IGBTs (2019)

TCAD simulation has been recognized as a powerful design tool for insulated gate bipolar transistors (IGBTs). In this work, excellent agreement between 3D TCAD simulations and experimental current-voltage characteristics were obtained in the up to 1000 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> region for IGBTs with scaled trench-gates. The results of 2D and 3D simulations are compared to discuss the difference in current-voltage characteristics and their physical origins. A method to evaluate the saturation current (J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Csat</sub> ) using a 2D simulation is also presented with an appropriate correction.
Data and Physics Driven Learning Models for Fast MRI -- Fundamentals and Methodologies from CNN, GAN to Attention and Transformers (2022)

Research studies have shown no qualms about using data driven deep learning models for downstream tasks in medical image analysis, e.g., anatomy segmentation and lesion detection, disease diagnosis and prognosis, and treatment planning. However, deep learning models are not the sovereign remedy for medical image analysis when the upstream imaging is not being conducted properly (with artefacts). This has been manifested in MRI studies, where the scanning is typically slow, prone to motion artefacts, with a relatively low signal to noise ratio, and poor spatial and/or temporal resolution. Recent studies have witnessed substantial growth in the development of deep learning techniques for propelling fast MRI. This article aims to (1) introduce the deep learning based data driven techniques for fast MRI including convolutional neural network and generative adversarial network based methods, (2) survey the attention and transformer based models for speeding up MRI reconstruction, and (3) detail the research in coupling physics and data driven models for MRI acceleration. Finally, we will demonstrate through a few clinical applications, explain the importance of data harmonisation and explainable models for such fast MRI techniques in multicentre and multi-scanner studies, and discuss common pitfalls in current research and recommendations for future research directions.
Frequency of Molecular and PET/CT Complete Remissions in Patients with Multiple Myeloma after Autologous Followed by Reduced-Intensity Allogeneic Stem Cell Transplants. (2004)

Abstract Despite recent advances multiple myeloma (MM) remains an incurable hemat&lt;/INS&gt;ologic malignancy with a median survival of about 4 years. Autologous stem cell transplant (SCT) followed by reduced-intensity allogeneic SCT (tandem auto-allo) is a promising new approach designed to combine maximal tumor reduction and graft-versus-myeloma effect. The definition of complete response (CR) after tandem auto-allo is based on conventional serologic, radiologic, and pathologic parameters (Blade criteria). Because more sensitive molecular and radionuclear techniques are available, we evaluated the predictive value of these techniques after tandem auto-allo. Our hypothesis is that minimal residual disease (MRD) after tandem auto-allo likely predicts relapse and that, if identified early, patients with MRD may be candidates for novel salvage therapies. We employed patient-specific clonal Ig gene polymerase chain reactions using marrow and blood cells, and whole-body positron-emission tomography/CT scans (PET/CT) to assess patients after tandem auto-allo. PCR detects and estimates molecular MRD. PET/CT may detect occult medullary and extramedullary (soft tissue) disease. In patients achieving CR by the Blade criteria, we determined the frequency with which PCR and PET/CT findings were concordant. We have treated 10 patients with MM, 8 men and 2 women, with tandem auto-allo. Median age was 50.5 years (range, 37–58). There was no peri-transplant mortality, but 3 patients have died of progressive disease at 278, 398, and 402 days post-allo. Seven patients are alive at a median of 337 days (101–1187) post-allo, one with persistent myeloma and one awaiting evaluation. The remaining 5 patients are in CR by standard criteria (immunofixation negative). Their current status is shown below. Age/Gender Status, days post-allo PCR (marrow) PET/CT 55M CR, d 1003 Neg on d 201, 924 Neg d 983 37W CR, d 632 Pos on d 452 Neg d 192 45M CR, d 337 Neg on d 88, 200 Equivocal d 222 39M CR, d 319 Pos on d 93, 177 Pos d 290 51M CR, d 172 Neg on d 104 Neg d 94 In sum, 2/5 have negative PCR and PET/CT findings; 1/5 has negative PCR and equivocal PET/CT findings; and 2/5 have positive PCR, one with positive PET/CT findings. Of note, all had negative PCR results using peripheral blood cells. The equivocal PET/CT showed low-level uptake in areas of prior myeloma in the pelvis. The positive PET/CT showed increased uptake in cervical and portacaval lymph nodes, but whether these findings represent occult myeloma is unclear. Overall, based on intention-to-treat in this small series, the frequency of CR with concordant PCR and PET findings is in the 20% to 30% range; and the frequency with which patients may become candidates for novel early salvage regimens is similar. A systematic approach using these methods after tandem auto-allo clearly merits further investigation.
Effect of lapatinib on accumulation of inactive HER2 at the cell membrane and on antibody-dependent cellular cytotoxicity (ADCC) mediated by trastuzumab: A novel mechanism for the enhanced effects of combined anti-HER2 therapy (2008)

3594 Background: Lapatinib is a HER2 tyrosine kinase inhibitor that has clinical activity in HER2 overexpressing (HER2+) breast cancer. In vitro and clinical studies have shown that lapatinib enhances the effects of the monoclonal antibody trastuzumab suggesting partially non-overlapping mechanisms of action. In order to dissect the differential mechanims of these agents, we have studied the effects of lapatinib and trastuzumab on receptor expression and signaling and have explored a new potential mechanism underlying the profound antitumor activity of the combination. Methods: HER2+ breast cancer cells SKBR3 and MCF7-HER2 were treated with lapatinib, trastuzumab or both. Assays of receptor expression, phosphorylation, signalling and tumor growth were performed. Trastuzumab-dependent cellular cytotoxicity was measured with different levels of HER2 expression and doses of lapatinib. Results: Lapatinib treatment of HER2+ breast cancer cells inhibited HER2 phosphorylation, prevented ubiquitination and resulted in a marked accumulation of inactive receptors at the cell surface. By contrast, trastuzumab caused enhanced HER2 phosphorylation, ubiquitination and degradation of the receptor. By immunoprecipitation and computational protein modelling techniques we further demonstrated that the lapatinib-induced accumulation of HER2 lead to stabilization of inactive HER2 homo- and hetero-dimers. Accumulation of HER2 induced by lapatinib and downregulation of HER2 mediated by trastuzumab were also observed in vivo, where the combination of the two agents triggered complete tumor remission in all cases after 10 days of treatment. Lapatinib-induced accumulation of HER2 at the cell surface markedly enhanced trastuzumab-mediated ADCC. Conclusions: Lapatinib results in a marked accumulation of inactive HER2 receptors at the cell surface both in vitro and in vivo. This increase in receptors number at the cell surface enhances ADCC by trastuzumab. We propose that this is a novel mechanism that may be clinically relevant and exploitable in the therapy of patients with HER2+ tumors. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Genentech
ANALYSIS OF THE DYNAMIC BEHAVIOUR OF MULTI-MESH SPUR AND HELICAL GEARS - APPLICATION TO THE DEFINITION OF OPTIMUM PROFILE RELIEFS IN AERONAUTICAL TRANSMISSIONS (2017)

This paper is focused on the modelling and analysis of vibrations and dynamic loads in aeronautical multi-mesh gears comprising several spatial gear arrangements (idler gears, several pinions on one shaft. Optimum profile modifications are sought by applying a metaheuristic Genetic Algorithm to the local quasi-static transmission errors under load associated with each individual mesh. It is shown that the resulting linear symmetric profile modifications all lie in the vicinity of the so-called analytical Master Curves initially defined for a single pinion-gear pair. The theory is applied to a 6-mesh aeronautical transmission and it is found that the proposed profile modifications can effectively reduce dynamic overloads and improve the vibrational behaviour of complex multi-mesh gears with different power circulations. Finally, it is shown that for systems submitted to several load levels, short optimal reliefs seem preferable with regard to vibration levels.
Improvements in level set segmentation of 3D small animal imagery (2007)

In this paper, we investigate several improvements to region-based level set algorithms in the context of segmenting x-ray CT data from pre-clinical imaging of small animal models. We incorporate a recently introduced signed distance preserving term into a region-based level set model and provide formulas for a semi-implicit finite difference implementation. We illustrate some pitfalls of topology preserving level sets and introduce the concept of connectivity preservation as a potential alternative. We illustrate the benefits of these improvements on phantom and real data.
40 Gb/s WDM Long-Haul Transmission on Non Slope-Matched Fiber (2002)

We demonstrate 1 Tb/s capacity at 40% spectral efficiency over 2055 km of non slope-matched fiber with 40 Gb/s channel data rate. Very high values of accumulated dispersion do not significantly affect system performance
Integrated chemical/biological treatment of paint stripper mixed waste: Metals toxicity and separation (1995)

The DOE complex has generated vast quantities of complex heterogeneous mixed wastes. Paint stripper waste (PSW) is a complex waste that arose from decontamination and decommissioning activities. It contains paint stripper, cheesecloth, cellulose-based paints with Pb and Cr, and suspect Pu. Los Alamos National Laboratory has 150--200 barrels of PSW and other national laboratories such as Rocky Flats Plant have many more barrels of heterogeneous waste. Few technologies exist that can treat this complex waste. Our approach to solving this problem is the integration of two established technologies: biodegradation and metals chelation.
Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS (2017)

Diffusion and interaction dynamics of molecules at the plasma membrane play an important role in cellular signaling and are suggested to be strongly associated with the actin cytoskeleton. Here we use superresolution STED microscopy combined with fluorescence correlation spectroscopy (STED-FCS) to access and compare the diffusion characteristics of fluorescent lipid analogues and GPI-anchored proteins (GPI-APs) in the live-cell plasma membrane and in actin cytoskeleton-free, cell-derived giant plasma membrane vesicles (GPMVs). Hindered diffusion of phospholipids and sphingolipids is abolished in the GPMVs, whereas transient nanodomain incorporation of ganglioside lipid GM1 is apparent in both the live-cell membrane and GPMVs. For GPI-APs, we detect two molecular pools in living cells; one pool shows high mobility with transient incorporation into nanodomains, and the other pool forms immobile clusters, both of which disappear in GPMVs. Our data underline the crucial role of the actin cortex in maintaining hindered diffusion modes of many but not all of the membrane molecules and highlight a powerful experimental approach to decipher specific influences on molecular plasma membrane dynamics.
Energy consumption in IP networks (2008)

A model of energy consumption in IP networks is used to estimate the energy consumption of the public Internet. Today’s Internet uses less than 1% of the available electricity supply. However, network energy consumption could grow substantially as access rates increase.
Transmitted/Founder and Chronic HIV-1 Envelope Proteins Are Distinguished by Differential Utilization of CCR5 (2012)

ABSTRACT Infection by HIV-1 most often results from the successful transmission and propagation of a single virus variant, termed the transmitted/founder (T/F) virus. Here, we compared the attachment and entry properties of envelope (Env) glycoproteins from T/F and chronic control (CC) viruses. Using a panel of 40 T/F and 47 CC Envs, all derived by single genome amplification, we found that 52% of clade C and B CC Envs exhibited partial resistance to the CCR5 antagonist maraviroc (MVC) on cells expressing high levels of CCR5, while only 15% of T/F Envs exhibited this same property. Moreover, subtle differences in the magnitude with which MVC inhibited infection on cells expressing low levels of CCR5, including primary CD4 + T cells, were highly predictive of MVC resistance when CCR5 expression levels were high. These results are consistent with previous observations showing a greater sensitivity of T/F Envs to MVC inhibition on cells expressing very high levels of CCR5 and indicate that CC Envs are often capable of recognizing MVC-bound CCR5, albeit inefficiently on cells expressing physiologic levels of CCR5. When CCR5 expression levels are high, this phenotype becomes readily detectable. The utilization of drug-bound CCR5 conformations by many CC Envs was seen with other CCR5 antagonists, with replication-competent viruses, and did not obviously correlate with other phenotypic traits. The striking ability of clade C and B CC Envs to use MVC-bound CCR5 relative to T/F Envs argues that the more promiscuous use of CCR5 by these Env proteins is selected against at the level of virus transmission and is selected for during chronic infection.