gebhart/patrepeval huggingface dataset:
Transformation ofTrichodermaSpp. With Plasmids Conferring Hygromycin B Resistance (1992)

Several Plasmids with different promoter sequences, all containing the HygB gene that confers resistance to the antibiotic hygromycin B, were evaluated for their ability to transform Trichoderma viride strain T105-227 Nie-. Plasmid pH1B, which contains a promoter sequence from Cochliobolus heterostrophus, was found to give the largest number of putative transformants. Transformation of T. harzianum strains T12-2 His- and T95-1 Lys- was attempted, and the time at which transformed protoplasts were exposed to hygromycin B was found to be critical. If hygromycin B was added before protoplasts had regenerated for at least 6 h, no transformants were obtained. However, if regeneration proceeded for more than 12 h, many nontransformed protoplasts formed thalli. Putative transformants were heterokaryotic. Even if thalli were grown in the presence of hygromycin B, the number of transformed nuclei was low; only 0.5 to 0.8% of conidia from putative transformants were capable of producing thalli in the presence of hygromycin B. Subcultures derived from single hygromycin B-resistant conidia were stable. Southern analysis indicated that the plasmid was integrated into the genome in either tandem repeat pattern or was single copy insertion.
The intrinsic resting state voice network in Parkinson's disease (2015)

Over 90 percent of patients with Parkinson's disease experience speech-motor impairment, namely, hypokinetic dysarthria characterized by reduced pitch and loudness. Resting-state functional connectivity analysis of blood oxygen level-dependent functional magnetic resonance imaging is a useful measure of intrinsic neural functioning. We utilized resting-state functional connectivity modeling to analyze the intrinsic connectivity in patients with Parkinson's disease within a vocalization network defined by a previous meta-analysis of speech (Brown et al., 2009). Functional connectivity of this network was assessed in 56 patients with Parkinson's disease and 56 gender-, age-, and movement-matched healthy controls. We also had item 5 and 18 of the UPDRS, and the PDQ-39 Communication subscale available for correlation with the voice network connectivity strength in patients. The within-group analyses of connectivity patterns demonstrated a lack of subcortical-cortical connectivity in patients with Parkinson's disease. At the cortical level, we found robust (homotopic) interhemispheric connectivity but only inconsistent evidence for many intrahemispheric connections. When directly contrasted to the control group, we found a significant reduction of connections between the left thalamus and putamen, and cortical motor areas, as well as reduced right superior temporal gyrus connectivity. Furthermore, most symptom measures correlated with right putamen, left cerebellum, left superior temporal gyrus, right premotor, and left Rolandic operculum connectivity in the voice network. The results reflect the importance of (right) subcortical nodes and the superior temporal gyrus in Parkinson's disease, enhancing our understanding of the neurobiological underpinnings of vocalization impairment in Parkinson's disease.
Additive manufacturing of graded B4C-Al cermets with complex shapes (2020)

Fabrication of boron carbide (B4C) parts through direct ink writing at room temperature has been demonstrated. The 3D printed B4C parts were made from aqueous, thixotropic ink consisting of B4C particles with a solid loading ranging from 50.0 to 59.3 vol%. The porous B4C parts were infiltrated with molten aluminum (Al) to form a dense B4C-Al cermet. Simple cubic samples with varied spacing between B4C filaments were printed to tailor the density profile within the part. The Rockwell hardness of such parts ranges from 20 to 90 Ra (60 kg) depending on the overall density of the B4C structure. Parts were printed with variable spacings between filaments to systematically determine the upper limit for Al infiltration (800 μm). Elemental analysis revealed a homogenous infiltration both between and within the filaments of 3D printed B4C.
Development of a Master Slave Combined Manipulator for Laparoscopic Surgery : Evaluation of the Operability for Suturing and Ligaturing Tasks (2002)

筆者らは, 腹腔鏡下手術を対象とし, マスタとスレーブが一体化され, 簡単・コンパクトでかつ操作性を優れた手術支援用マニピュレータを開発している。試作した一体型マスタとスレーブマニピュレータについて, ファントムを用い腹腔鏡下で彎曲針による縫合結紮作業を実施し, 従来の鉗子では不可能な方向からの縫合作業が容易であることが確認できた。さらに, 縫合時の各関節角動作データ, 作業時間および作業精度を取得し, 操作性の定量的評価を行った。
Real-world performance, long-term efficacy, and absence of bias in the artificial intelligence enhanced electrocardiogram to detect left ventricular systolic dysfunction (2022)

The artificial intelligence-enhanced electrocardiogram to detect left ventricular systolic dysfunction is stable over time in the absence of retraining and robust with respect to multiple variables including time, patient race, and electrocardiogram features.
Robust current control insensitive to gain deviation and offset of inverter DC-link current sensor for SPMSM (2014)

An AC servomotor is operated by current sensors. Owing to cost implications, it is often operated by an inverter system based on single DC-link current sensor. However, a current sensor sometimes has offset and gain variation caused by secular and thermal variation. When surface permanent magnet synchronous motor (SPMSM) drive system has the offset and the gain variation of current sensor, SPMSM has the current ripples and torque ripples. This paper proposes a new robust current control system insensitive to deviation and offset of current sensor for SPMSM. The proposed system tunes the current measurement gain deviation and realizes robust current control system. The proposed method suppresses q axis current errors by tuning the current measurement gains. Simulation results and experimental results confirm that the proposed method well suppresses the current sensor offset and the current sensor gain variation. Hence, the robust current control for SPMSM is always completed.
Improved Device Performances in Phosphorescent Organic Light-Emitting Diodes by Microcavity Effects (2012)

In order to improve the external quantum efficiency of organic light-emitting diodes (OLEDs), we purpose an anode which has a structure of indium tin oxide (ITO)/Ag/ITO, in which the Ag layer has a function of micro-cavity inducing reflector. In order to maximize the microcavity effect the thicknesses of the hole transport layers of blue and red phosphorescent OLEDs (PhOLEDs) were deduced using simulations. By the use of our optically designed anode, it was possible to achieve approximately 50% improvements in the external quantum efficiency.
Effect of Fluoride-based Plasma Treatment on the Performance of AlGaN/GaN MISFET (2016)

This paper demonstrates the effect of fluoride-based plasma treatment on the performance of Al2O3/AlGaN/GaN metal-insulator-semiconductor heterostructure field effect transistors (MISHFETs) with a T-shaped gate length of 0.20 μm. For the fabrication of the MISHFET, an Al2O3 layer as a gate dielectric was deposited using atomic layer deposition, which greatly decreases the gate leakage current, followed by the deposition of the silicon nitride layer. The silicon nitride layer on the gate foot region was then selectively removed through a reactive ion etching technique using CF4 plasma. The etching process was continued for a longer period of time even after the complete removal of the silicon nitride layer to expose the Al2O3 gate dielectric layer to the plasma environment. The thickness of the Al2O3 gate dielectric layer was slowly reduced during the plasma exposure. Through this plasma treatment, the device exhibited a threshold voltage shift of 3.1 V in the positive direction, an increase of 50 mS/mm in trans conductance, a degraded off-state performance and a larger gate leakage current compared with that of the reference device without a plasma treatment.
Inkjet based 3D Printing of bespoke medical devices that resist bacterial biofilm formation (2020)

Abstract We demonstrate the formulation of advanced functional 3D printing inks that prevent the formation of bacterial biofilms in vivo . Starting from polymer libraries, we show that a biofilm resistant object can be 3D printed with the potential for shape and cell instructive function to be selected independently. When tested in vivo , the candidate materials not only resisted bacterial attachment but drove the recruitment of host defences in order to clear infection. To exemplify our approach, we manufacture a finger prosthetic and demonstrate that it resists biofilm formation – a cell instructive function that can prevent the development of infection during surgical implantation. More widely, cell instructive behaviours can be ‘dialled up’ from available libraries and may include in the future such diverse functions as the modulation of immune response and the direction of stem cell fate.
Functional Study of the C-Terminal Part of the Hepatitis C Virus E1 Ectodomain (2018)

In the hepatitis C virus (HCV) envelope glycoproteins E1 and E2, which form a heterodimer, E2 is the receptor binding protein and the major target of neutralizing antibodies, whereas the function of E1 remains less characterized. To investigate E1 functions, we generated a series of mutants in the conserved residues of the C-terminal region of the E1 ectodomain in the context of an infectious clone. We focused our analyses on two regions of interest. The first region is located in the middle of the E1 glycoprotein (between amino acid [aa] 270 and aa 291), which contains a conserved hydrophobic sequence and was proposed to constitute a putative fusion peptide. The second series of mutants was generated in the region from aa 314 to aa 342 (the aa314-342 region), which has been shown to contain two α helices (α2 and α3) by nuclear magnetic resonance studies. Of the 22 generated mutants, 20 were either attenuated or noninfectious. Several mutations modulated the virus's dependence on claudin-1 and the scavenger receptor BI coreceptors for entry. Most of the mutations in the putative fusion peptide region affected virus assembly. Conversely, mutations in the α-helix aa 315 to 324 (315-324) residues M318, W320, D321, and M322 resulted in a complete loss of infectivity without any impact on E1E2 folding and on viral assembly. Further characterization of the W320A mutant in the HCVpp model indicated that the loss of infectivity was due to a defect in viral entry. Together, these results support a role for E1 in modulating HCV interaction with its coreceptors and in HCV assembly. They also highlight the involvement of α-helix 315-324 in a late step of HCV entry.<b>IMPORTANCE</b> HCV is a major public health problem worldwide. The virion harbors two envelope proteins, E1 and E2, which are involved at different steps of the viral life cycle. Whereas E2 has been extensively characterized, the function of E1 remains poorly defined. We characterized here the function of the putative fusion peptide and the region containing α helices of the E1 ectodomain, which had been previously suggested to be important for virus entry. We could confirm the importance of these regions for the virus infectivity. Interestingly, we found several residues modulating the virus's dependence on several HCV receptors, thus highlighting the role of E1 in the interaction of the virus with cellular receptors. Whereas mutations in the putative fusion peptide affected HCV infectivity and morphogenesis, several mutations in the α2-helix region led to a loss of infectivity with no effect on assembly, indicating a role of this region in virus entry.
Breaking Through the Multi-Mesa-Channel Width Limited of Normally Off GaN HEMTs Through Modulation of the Via-Hole-Length (2017)

We present new normally off GaN high-electron-mobility transistors (HEMTs) that overcome the typical limitations in multi-mesa-channel (MMC) width through modulation of the via-hole-length to regulate the charge neutrality screen effect. We have prepared enhancement-mode (E-mode) GaN HEMTs having widths of up to 300 nm, based on an enhanced surface pinning effect. E-mode GaN HEMTs having MMC structures and widths as well as via-hole-lengths of 100 nm/2 μm and 300 nm/6 μm, respectively, exhibited positive threshold voltages (V <sub>th</sub>) of 0.79 and 0.46 V, respectively. The on-resistances of the MMC and via-hole-length structures were lower than those of typical tri-gate nanoribbon GaN HEMTs. In addition, the devices not only achieved the E-mode but also improved the power performance of the GaN HEMTs and effectively mitigated the device thermal effect. We controlled the via-hole-length sidewall surface pinning effect to obtain the E-mode GaN HEMTs. Our findings suggest that via-hole-length normally off GaN HEMTs have great potential for use in next-generation power electronics.
Glucose promotes regulatory T cell differentiation to maintain intestinal homeostasis (2022)

Glucose, the critical energy source in the human body, is considered a potential risk factor in various autoimmune diseases when consumed in high amounts. However, the roles of glucose at moderate doses in the regulation of autoimmune inflammatory diseases and CD4<sup>+</sup> T cell responses are controversial. Here, we show that while glucose at a high concentration (20% w/v) promotes intestinal inflammation, it suppresses colitis at a moderate dose (6% w/v), which increases the proportion of intestinal regulatory T (Treg) cells but does not affect effector CD4<sup>+</sup> T cells. Glucose treatment promotes Treg cell differentiation but it does not affect Treg stability. Feeding glucose alters gut microbiota compositions, which are not involved in the glucose induction of Treg cells. Glucose promotes aryl hydrocarbon receptor (AhR) activation to induce Treg polarization. These findings reveal the different effects of glucose at different doses on the intestinal immune response.
Distributed parallel image signal extrapolation framework using Message Passing Interface (2016)

This paper introduces a framework for distributed parallel image signal extrapolation. Since high-quality image signal processing often comes along with a high computational complexity, a parallel execution is desirable. The proposed framework allows for the application of existing image signal extrapolation algorithms without the need to modify them for a parallel processing. The unaltered application of existing algorithms is achieved by dividing input images into overlapping tiles which are distributed to compute nodes via Message Passing Interface. In order to keep the computational overhead low, a novel image tiling algorithm is proposed. Using this algorithm, a nearly optimum tiling is possible at a very small processing time. For showing the efficacy of the framework, it is used for parallelizing a high-complexity extrapolation algorithm. Simulation results show that the proposed framework has no negative impact on extrapolation quality while at the same time offering good scaling behavior on compute clusters.
Uncommon Behavior of Li Doping Suppresses Oxygen Redox in P2‐Type Manganese‐Rich Sodium Cathodes (2021)

Utilizing both cationic and anionic oxygen redox reactions is regarded as an important approach to exploit high-capacity layered cathode materials with earth abundant elements. It has been popular strategies to effectively elevate the oxygen redox activities by Li-doping to introduce unhybridized O 2p orbitals in Na<sub>x</sub> MnO<sub>2</sub> -based chemistries or enabling high covalency transition metals in P2-Na<sub>0.66</sub> Mn<sub>x</sub> TM<sub>1-</sub> <sub>x</sub> O<sub>2</sub> (TM = Fe, Cu, Ni) materials. Here, the effect of Li doping on regulating the oxygen redox activities P2-structured Na<sub>0.66</sub> Ni<sub>0.25</sub> Mn<sub>0.75</sub> O<sub>2</sub> materials is investigated. Systematic X-ray characterizations and ab initio simulations have shown that the doped Li has uncommon behavior in modulating the density of states of the neighboring Ni, Mn, and O, leading to the suppression of the existing oxygen and Mn redox reactivities and the promotion of the Ni redox. The findings provide a complementary scenario to current oxygen redox mechanisms and shed lights on developing new routes for high-performance cathodes.
CD30-Targeted Therapy with Brentuximab Vedotin Combined with Donor Lymphocyte Infusions Induce Sustained Clinical Remissions and Tumor Specific Immunity in a Series of Patients with Relapsed Hodgkin Lymphoma After Allogeneic Stem Cell Transplantation (2012)

Abstract Abstract 4213 Introduction Hodgkin lymphoma (HL) is curable in a high proportion of patients. However, relapsed HL remains a therapeutic challenge especially if high-dose chemotherapy is not possible or the lymphoma has even relapsed after this salvage therapy. In such situations, allogeneic stem cell transplantation (alloSCT) is a potential curative option in which the graft-versus-lymphoma (GvL) effect can lead to immune mediated sustained tumor control. However, in the early phase after alloSCT, the risk of relapse is increased due to attenuated immune cell activity. In this situation, conventional systemic cytotoxic therapies are usually associated with a high mortality. We hypothesized that treatment with brentuximab vedotin would be a promising approach for relapsed HL after alloSCT as it selectively targets the lymphoma cells via CD30 and might enhance a GvL response by the induction of immunogenic cell death. Moreover, the combination of this targeted therapy with donor lymphocyte infusions (DLI) would have the potential to further increase the GvL effect. Methods Four patients with relapsed HL after alloSCT were consecutively treated from March 2011 to March 2012 with brentuximab vedotin and DLI in an alternating regimen. All patients were included into a named-patient-program (Millenium, USA) and gave their written consent. Blood collection and immune cell in-vitro analyses were approved by the institutional review board. Evaluation of treatment response was performed clinically and with computed tomography scans following established criteria. Moreover, metabolic changes were analyzed by FDG-PET/CT scans. To assess the induction of a GvL effect, we developed an in-vitro method using co-cultures of patient PBMCs (pre and post treatment) and well characterized CD30+ HL cell lines and controls as surrogate targets. Results Clinical evaluation showed that all four patients had marked clinical and metabolic responses with a median duration of disease control of at least 463 days (range 259–1189) after treatment initiation which is still ongoing in three patients. Sensory polyneuropathy and mild thrombopenia were the most common side effects. Assessment of immunologic changes showed no significant tumor-specific T-cell reactivity prior to treatment. In contrast, a significant increase of HL-specific T cell activation could be observed in-vitro in all patients after treatment. Reactive HL-specific T cells mainly co-expressed CD161 and CD4 suggesting a TH17 like phenotype. Conclusion Taken together, we present evidence that CD30-targeted Hodgkin lymphoma therapy with brentuximab vedotin and DLI induces sustained clinical responses and tumor-specific immunity in an allogeneic setting which warrants further investigation in a larger population. Disclosures: Engert: Takeda Millenium: Consultancy, Honoraria, Research Funding.
Abstract 3059: Identification and validation of an Aspergillusnidulanssecondary metabolite derivative as an inhibitor of the Musashi1-RNA interaction (2019)

RNA-binding protein Musashi-1 (MSI1) is a key regulator of several stem cell populations. It is involved in tumor proliferation and maintenance, and it regulates target mRNAs at the translational level. The known mRNA targets of MSI1 include Numb, APC and P21WAF-1, key regulators of Notch, Wnt signaling and cell cycle progression, respectively. In this study, we aim to identify small molecule inhibitors of MSI1-mRNA interaction thus blocking the growth of cancer cells with high levels of MSI1. Using a fluorescence polarization (FP) assay, we screened small molecules from several chemical libraries for those that disrupt the binding of MSI1 to its consensus RNA binding site. Two clusters of hit compounds have been identified, one of which is composed of derivatives of secondary metabolites from Aspergillus nidulans. The top hit, Aza-9, from this cluster was further validated by surface plasmon resonance and nuclear magnetic resonance which revealed that Aza-9 binds to MSI1 directly, in the RNA binding pocket. Next, we tested whether Aza-9 has anti-cancer potential in cells and whether such activities work through MSI1. Due to poor cellular uptake, we used PEGylated liposomes to facilitate Aza-9 entry into the cells. Aza-9-lipo inhibits colon cancer cell proliferation, induces apoptosis and autophagy, and down-regulates Notch/Wnt signaling in colon cancer cell lines. In conclusion, we identified a series of potential lead compounds for inhibiting MSI1 function while establishing a framework for identifying small molecule inhibitors of RNA binding proteins using FP-based screening methodology.Citation Format: Lan Lan, Jiajun Liu, Amber Amith, Carl Appelman, Xiaoqing Wu, Ke Li, Anuradha Roy, Ragul Gowthaman, John Karanicolas, Amber Somoza, Clay Wang, Berl Oakley, Roberto De Guzman, Kristi Neufeld, Liang Xu. Identification and validation of an Aspergillus nidulanssecondary metabolite derivative as an inhibitor of the Musashi1-RNA interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3059.
A compact snapshot multispectral imager with a monolithically integrated per-pixel filter mosaic (2014)

The adoption of spectral imaging by industry has so far been limited due to the lack of high speed, low cost and compact spectral cameras. Moreover most state-of-the-art spectral cameras utilize some form of spatial or spectral scanning during acquisition, making them ill-suited for analyzing dynamic scenes containing movement. This paper introduces a novel snapshot multispectral imager concept based on optical filters monolithically integrated on top of a standard CMOS image sensor. It overcomes the problems mentioned for scanning applications by snapshot acquisition, where an entire multispectral data cube is sensed at one discrete point in time. This is enabled by depositing interference filters per pixel directly on a CMOS image sensor, extending the traditional Bayer color imaging concept to multi- or hyperspectral imaging without a need for dedicated fore-optics. The monolithic deposition leads to a high degree of design flexibility. This enables systems ranging from application-specific, high spatial resolution cameras with 1 to 4 spectral filters, to hyperspectral snapshot cameras at medium spatial resolutions and filters laid out in cells of 4x4 to 6x6 or more. Through the use of monolithically integrated optical filters it further retains the qualities of compactness, low cost and high acquisition speed, differentiating it from other snapshot spectral cameras.