gebhart/patrepeval huggingface dataset:
Ge Implantation to Improve Crystallinity and Productivity for Solid Phase Epitaxy Prepared by Atomic Mass Unit Cross Contamination-Free Technique (2006)

Germanium (Ge) ion implantation was investigated for crystallinity enhancement during solid phase epitaxial (SPE) regrowth. Electron back-scatter diffraction (EBSD) measurement showed numerical increase of 19% of (100) signal, which might be due to the effect of pre-amorphization implantation (PAI) on silicon layer. On the other hand, electrical property such as off-leakage current of n-channel metal oxide semiconductor (NMOS) transistor degraded in specific regions of wafers. It was confirmed that arsenic (As) atoms were incorporated into channel area during Ge ion implantation. Since the equipment for Ge PAI was using several source gases such as BF3 and AsH3, atomic mass unit (AMU) contamination during PAI of Ge with AMU 74 caused the incorporation of As with AMU 75 which resided in arc-chamber and other parts of the equipment. It was effective to use Ge isotope of AMU 72 to suppress AMU contamination. It was effective to use enriched Ge source gas with AMU 72 in order to improve productivity.
Impact of Imbalance Usage of Social Networking Sites on Families (2015)

With the proliferation of social networking sites (SNSs) such as Facebook and Google+, investigating the impact of SNSs on our lives has become an important research area in recent years. Though SNS usage plays a key role in connecting people with friends and families from distant places, SNSs also bring concern for families. We focus on imbalance SNS usage, i.e., an individual remains busy in using SNSs when her family member is expecting to spend time with her. More specifically, we investigate the cause and pattern of imbalance SNS usage and how the emotion of family members may become affected, if they use SNSs in an imbalanced way in a regular manner. This paper is the first attempt to identify the relationship between an individual's imbalance SNS usage and the emotion of her family member in the context of a developing country.
E114 Rational Design and Clinical Development of New Adjuvants (2013)

Safe and effective adjuvants for prophylactic and therapeutic vaccine use are resulting from the identification and optimizing formulations of small molecules. For a new adjuvant to be widely accepted and used, important considerations include non-clinical safety and efficacy, understanding of mechanism of action, and manufacturability and stability of the active ingredients and excipients used in the final adjuvant composition. Effectively engaging macrophages and dendritic cells (DC), leading to T cell responses is essential for developing a new generation of T cell vaccines (e.g. tuberculosis, malaria, HIV), as well as for improving the quality and duration of antibody responses (influenza, HPV, HIV, etc.). Among the most advanced approaches to new adjuvant development consist of using TLR ligands (TLRL) that, when properly formulated, can be effective when used in minimal amounts. We have developed formulations of our lead TLR4L, GLA, and have evaluated a variety of these, including oil/water emulsions, micellar, and liposomal, in non-clinical and clinical studies. When properly formulated, GLA has the ability to focus toward Th1 responses, induce CD8 T cells, and enhance and broadened specific antibody responses. Clinical trials using formulated GLA have been have completed using seasonal and pandemic influenza, and schistosoma antigens, and ongoing are trials in HIV, tuberculosis, leishmaniasis, malaria, pandemic influenza, and a study to examine innate responses to adjuvant alone. Excellent safety and immunogenicity profiles have been observed in non-clinical and clinical studies.
Sphingosine kinase: apoptosis regulating enzyme and chemotherapy target in prostate cancer (2007)

Recently we showed that inhibition of a known oncogene sphingosine kinase (SK) is linked to chemo‐sensitivity of prostate cancer cells. Currently we proposed a novel pharmacological SK inhibitor as a chemosensitizer in prostate cancer cell and mouse models. Pharmacological SK inhibition with novel, highly specific inhibitor induced cell death in PC‐3 cells in a dose‐dependent manner. Cell death, triggered by SKI had apoptotic features, as confirmed by fluorescent microscopy and flow cytometry, and is mediated by caspase‐8, ‐7 and ‐3 activation, subsequently followed by PARP cleavage. Similar effect an be achieved using siRNA to SK1 whereas enforced expression of sphingosine kinase rendered cells resistant to these treatments. Previously we found that chemoresistance of PC‐3 cells is linked to the absence of SK inhibition. Here we report that pretreatment of PC‐3 cells with small, non‐toxic doses of SKI or with siRNA to SK overcomes chemoresistance of PC‐3 cells. SKI appears to have no general toxicity in vivo. Mice orthotopically engrafted with PC‐3/GFP fluorescent cells were treated weekly with either SKI, camptothecin and both SKI and camptothecin together. SKI alone induced small tumor diminishment, however twice potentiated the effect of camptothecin. SKI treatment also reduced on 35% the number of micrometastases, assessed by GFP fluorescence. Our results demonstrate a novel SK inhibitor as an efficient chemosensitizer both in cell and animal prostate cancer models.
Optical fiber long-period grating humidity sensor utilizing PEO/CoCl 2 outcladding overlayers (2005)

We describe a fiber optic humidity sensor comprising a moisture - sensitive overlay on a long period fiber grating (LPFG), tuned at the 1.5 microns band. The hygrosensitive material overlaid was poly(ethylene oxide)/CoCl<sub>2</sub> hybrid containing 10 % wt CoCl<sub>2</sub> in the form of micro- and nano-particles synthesized in situ in the polymer of 50000 molecular weight. A thin overlay of the material is deposited from an aqueous solution on the unclad region of the LPFG and upon exposure to different ambient humidity levels its spectral properties are modified. The experimental results obtained, show changes of the spectral resonance notch and the transmission strength of the LPFG. The material parameters associated with the sensing mechanism may include those of refractive index, absorption and morphological alterations of the overlaid material. Relative humidity (RH) variations in the range from 50% to 95% can been detected with a resolution better than 0.2% RH. The response time constant is found of the order of few hundred milliseconds.
Open Imputation Server provides secure Imputation services with provable genomic privacy (2021)

Abstract Summary As DNA sequencing data is available for personal use, genomic privacy is becoming a major challenge. Nevertheless, high-throughput genomic data analysis outsourcing is performed using pipelines that tend to overlook these challenges. Results We present a client-server-based outsourcing framework for genotype imputation, an important step in genomic data analyses. Genotype data is encrypted by the client and encrypted data are used by the server that never observes the data in plain. Cloud-based framework can benefit from virtually unlimited computational resources while providing provable confidentiality. We demonstrate server’s utility from several aspects using genotype dataset from the 1000 Genomes datasets. First, we benchmark the accuracy of common variant imputation in comparison to BEAGLE, a state-of-the-art imputation method. We also provide the detailed time requirements of the server to showcase scaling of time usage in different steps of imputation. We also present a simple correlation metric that can be used to estimate imputation accuracy using only the reference panels. This is important for filtering the variants in downstream analyses. As a further demonstration and a different use case, we performed a simulated genomewide association study (GWAS) using imputed and known genotypes and highlight potential utility of the server for association studies. Overall, our study present multiple lines of evidence for usability of secure imputation service. Availability Server is publicly available at https://www.secureomics.org/OpenImpute . Users can anonymously test and use imputation server without registration. Contact Arif.O.Harmanci@uth.tmc.edu
A Pilot Study of the Sludge Recycling Enhanced Coagulation–Ultrafiltration Process for Drinking Water: The Effects of Sludge Recycling Ratio and Coagulation Stirring Strategy (2017)

The pilot-scale study on a sludge recycling enhanced coagulation–ultrafiltration (UF) process for surface water treatment is investigated in this paper. The impact of the sludge recycling ratio and coagulation stirring strategy on removal, sedimentation efficiency, and membrane fouling control was studied in this work. Sludge recycling ratios of 0%, 5%, 10%, 15%, and 20% were applied, and the optimal ratio was found to be 10%. Moreover, four stirring strategies were also applied, and the best stirring strategy for coagulation was found to be rapid mixing (velocity gradient: 280 s−1), which is quite different from the coagulation stirring strategy without sludge recycling. This suggests that the adsorption effect of sludge could play a leading role during the procedure. Moreover, shortening the coagulation process makes it possible to reduce energy consumption.
Differentiation of EL4 lymphoma cells by tumoral environment is associated with inappropriate expression of the large chondroitin sulfate proteoglycan PG-M and the tumor-associated antigen HTgp-175 (1998)

Progression to malignancy of transformed cells involves complex genetic alterations and aberrant gene expression patterns. While aberrant gene expression is often caused by alterations in individual genes, the contribution of the tumoral environment to the triggering of this gene expression is less well established. The stable but heterogeneous expression in cultured EL4/13 cells of a novel tumor-associated antigen, designated as HTgp-175, was chosen for the investigation of gene expression during tumor formation. Homogeneously HTgp-175-negative EL4/13 cells, isolated by cell sorting or obtained by subcloning, acquired HTgp-175 expression as a result of tumor formation. The tumorigenicity of HTgp-175-negative vs. HTgp-175-positive EL4 variants was identical, indicating that induction but not selection accounted for the phenotypic switch from HTgp-175-negative to HTgp-175-positive. Although mutagenesis experiments showed that the protein was not essential for tumor establishment, tumor-derived cells showed increased malignancy, linking HTgp-175 expression with genetic changes accompanying tumor progression. This novel gene expression was not an isolated event, since it was accompanied by ectopic expression of the large chondroitin sulfate proteoglycan PG-M and of normal differentiation antigens. We conclude that signals derived from the tumoral microenvironment contribute significantly to the aberrant gene expression pattern of malignant cells, apparently by fortuitous activation of differentiation processes and cause expression of novel differentiation antigens as well as of inappropriate tumor-associated and ectopic antigens.
Analysis of the role of theAspergillus nigeraminolevulinic acid synthase (hemA) gene illustrates the difference between regulation of yeast and fungal haem- and sirohaem-dependent pathways (2012)

To increase knowledge on haem biosynthesis in filamentous fungi like Aspergillus niger, pathway-specific gene expression in response to haem and haem intermediates was analysed. This analysis showed that iron, 5'-aminolevulinic acid (ALA) and possibly haem control haem biosynthesis mostly via modulating expression of hemA [coding for 5'-aminolevulinic acid synthase (ALAS)]. A hemA deletion mutant (ΔhemA) was constructed, which showed conditional lethality. Growth of ΔhemA was supported on standard nitrate-containing media with ALA, but not by hemin. Growth of ΔhemA could be sustained in the presence of hemin in combination with ammonium instead of nitrate as N-source. Our results suggest that a branch-off within the haem biosynthesis pathway required for sirohaem synthesis is responsible for lack of growth of ΔhemA in media containing nitrate as sole N-source, because of the requirement of sirohaem for nitrate assimilation, as a cofactor of nitrite reductase. In contrast to the situation in Saccharomyces cerevisiae, cysteine, but not methionine, was found to further improve growth of ΔhemA. These results demonstrate that A. niger can use exogenous hemin for its cellular processes. They also illustrate important differences in regulation of haem biosynthesis and in the role of haem and sirohaem in A. niger compared to S. cerevisiae.
The Regioselectivity of the Cycloadditions of Ketenes with N-Alkyl- and N-Arylnitrones (1978)

Cyclopentamethyleneketene, m-butylcarbethoxyketene, and tert-butylcyanoketene react with N-arylnitrones to form oxazolidinones while t&&-butylcyanoketene reacts with N-methyl-and N-ethylnitrones to afford isoxazolidinones.Our interest in the reactions of ketenes with N-arylimines, ketenimines, 1 azines and N-alkylimines led us to investigate the cycloadditions of ketenes
Understanding of Trap-Assisted Tunneling Current - Assisted by Oxygen Vacancies in RuOx/SrTiO3/TiN MIM Capacitor for the DRAM Application (2012)

A transient leakage current was measured as a function of time for thin (~9 nm) strontium titanate (STO) capacitor dielectrics with RuOx as a bottom electrode and TiN as a top electrode at different temperatures under constant direct current (DC) bias stress. With the space-charge-limited (SCL) current theory, the mobility of oxygen vacancies (VO) and the activation energy (E0) of VO were extracted. By closely examining the time-zero current-voltage (I-V) curves for a positively and a negatively held DC bias conditions before and after the stresses, an understanding of trap-assisted-tunneling (TAT) current, initiated by oxygen vacancies (VO) is presented. Based on this understanding, a way to further reduce the leakage current for a sub-10 nm dielectric film is provided.
High PDGFRb Expression Predicts Resistance to Radiotherapy in DCIS within the SweDCIS Randomized Trial (2021)

Results suggest high stromal PDGFRb expression as a novel biomarker identifying DCIS patients who are refractory to standard whole-breast adjuvant RT. The data imply previously unrecognized fibroblast-mediated modulation of radiosensitivity of DCIS, which should be further explored from mechanistic and targeting perspectives.
SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells (2014)

The molecular determinants that render specific populations of normal cells susceptible to oncogenic reprogramming into self-renewing cancer stem cells are poorly understood. Here, we exploit T-cell acute lymphoblastic leukemia (T-ALL) as a model to define the critical initiating events in this disease. First, thymocytes that are reprogrammed by the SCL and LMO1 oncogenic transcription factors into self-renewing pre-leukemic stem cells (pre-LSCs) remain non-malignant, as evidenced by their capacities to generate functional T cells. Second, we provide strong genetic evidence that SCL directly interacts with LMO1 to activate the transcription of a self-renewal program coordinated by LYL1. Moreover, LYL1 can substitute for SCL to reprogram thymocytes in concert with LMO1. In contrast, inhibition of E2A was not sufficient to substitute for SCL, indicating that thymocyte reprogramming requires transcription activation by SCL-LMO1. Third, only a specific subset of normal thymic cells, known as DN3 thymocytes, is susceptible to reprogramming. This is because physiological NOTCH1 signals are highest in DN3 cells compared to other thymocyte subsets. Consistent with this, overexpression of a ligand-independent hyperactive NOTCH1 allele in all immature thymocytes is sufficient to sensitize them to SCL-LMO1, thereby increasing the pool of self-renewing cells. Surprisingly, hyperactive NOTCH1 cannot reprogram thymocytes on its own, despite the fact that NOTCH1 is activated by gain of function mutations in more than 55% of T-ALL cases. Rather, elevating NOTCH1 triggers a parallel pathway involving Hes1 and Myc that dramatically enhances the activity of SCL-LMO1 We conclude that the acquisition of self-renewal and the genesis of pre-LSCs from thymocytes with a finite lifespan represent a critical first event in T-ALL. Finally, LYL1 and LMO1 or LMO2 are co-expressed in most human T-ALL samples, except the cortical T subtype. We therefore anticipate that the self-renewal network described here may be relevant to a majority of human T-ALL.
Site-Specific Modification of Single-Chain Antibody Fragments for Bioconjugation and Vascular Immunotargeting (2017)

The conjugation of antibodies to drugs and drug carriers improves delivery to target tissues. Widespread implementation and effective translation of this pharmacologic strategy awaits the development of affinity ligands capable of a defined degree of modification and highly efficient bioconjugation without loss of affinity. To date, such ligands are lacking for the targeting of therapeutics to vascular endothelial cells. To enable site-specific, click-chemistry conjugation to therapeutic cargo, we used the bacterial transpeptidase, sortase A, to attach short azidolysine containing peptides to three endothelial-specific single chain antibody fragments (scFv). While direct fusion of a recognition motif (sortag) to the scFv C-terminus generally resulted in low levels of sortase-mediated modification, improved reaction efficiency was observed for one protein, in which two amino acids had been introduced during cloning. This prompted insertion of a short, semi-rigid linker between scFv and sortag. The linker significantly enhanced modification of all three proteins, to the extent that unmodified scFv could no longer be detected. As proof of principle, purified, azide-modified scFv was conjugated to the antioxidant enzyme, catalase, resulting in robust endothelial targeting of functional cargo in vitro and in vivo.
Instrument calibration reduction using signal validation (1993)

Instrument calibration reduction is an application for signal validation. Because instrument recalibration is generally required for each fuel cycle and because many instruments are normally inaccessible, calibration reduction is beneficial from the decreased manpower requirements (during an already busy fuel outage) and the reduction in personnel exposure. Calibration reduction affords an excellent opportunity to exploit the capabilities of signal validation. In-plant testing us under way at an operation pressuried water reactor using a signal-validation-based calibration reduction system. This work has shown that on-line monitoring of instrument channels in nuclear power plants can help segregate the channels that are drifting from those that are not.
Re‐endothelialization of non‐detergent decellularized porcine vessels (2020)

Tissue engineering utilizes an interdisciplinary approach to generate constructs for the treatment and repair of diseased organs. Generation of small vessels as vascular grafts or as envisioned central vessel for vascularized constructs is still a challenge. Here, the decellularization of porcine vessels by a non-detergent based protocol was developed and investigated. Perfusion-decellularization with sodium hydroxide solution resulted in removal of cellular material throughout the whole length of the vessel while preserving structural and mechanical integrity. A re-endothelialization of the retrieved matrix with human umbilical vein endothelial cells and cardiac endothelial cells was achieved through rotation-based seeding employing a custom-made bioreactor. A confluent monolayer was detected on the entire luminal surface. Thus, a non-detergent-based decellularization method allowing the re-endothelialization of the luminal surface was developed in this study, thereby paving the way for future implementation of the resulting construct as vascular graft or as central vessel for tissue engineered constructs in need of a perfusion system with readily available anastomosis sites.
Development of a Seasonal Thermochemical Storage System (2012)

In our laboratories, a seasonal thermochemical storage system for dwellings and offices is being designed and developed. Based on a thermochemical sorption reaction, space heating, cooling and generation of domestic hot water will be achieved with up to 100% renewable energy, by using solar energy and waste heat. Development of the reactor and its components (adsorber/desorber, evaporator/condenser) as well as on the active material are described, and indications for further improvement are given. Simulations and experiments yield promising results for further development in demonstrators and field tests of the system set-up, and our newly developed enhanced active material yields promising results exhibiting high storage capacity, good reversibility and ease of use.
B232 AREVA's Filtered Containment Venting System (FCVS) : Basic Design, Performance and Verification Test of FCVS for BWRs (2014)

After the great earthquake and a tsunami as consequence March 11, 2011, a severe accident happened at nuclear power plant Fukushima Daiichi. The severe accident lead to core damage and containment failure and finally to large release of radioactive substances to the environment. As part of the severe accident management and to reinforce the mitigation concepts against a containment failure, the Filtered Containment Venting System (FCVS) will be introduced at Japanese nuclear power plants, to have a possibility to depressurize safely and reliable the containment via a filtered process. This paper describes AREVA FCVS technology and its application for Japanese BWRs and also the background of the qualification and the licensing approach.
The effect of the phase of transmission on contrast agent echoes (1998)

Ultrasound contrast agents consist of a gas bubble, encapsulated by a shell for stabilization. The shell dampens the fluctuations in the bubble radius when insonified. The detection of contrast microbubbles during a medical examination can indicate whether a region is perfused with blood. Here, the authors consider the effect of the phase of sonification signal on the backscatter by the bubble echo. By transmitting two short pulses of ultrasound with opposite phases, the authors demonstrate that a unique pair of echoes can be generated by a single microbubble, and that the properties of these echoes may be useful in the discrimination of bubble and tissue echoes. Specifically, the significant echo amplitude begins coincident with each transmitted rarefactional half-cycle, and the mean frequency of this echo depends on the transmitted phase. When rarefaction is transmitted first for a 2.25 MHz signal, the mean frequency is 0.8 MHz higher for an albumin-shelled bubble and 0.9 MHz higher for a lipid-shelled bubble. The experimental results agree with the predictions of the Gilmore-Akulichev equation.