gebhart/patrepeval huggingface dataset:
Three‐Dimensional Nanostructured Indium‐Tin‐Oxide Electrodes for Enhanced Performance of Bulk Heterojunction Organic Solar Cells (2014)

A three‐dimensional indium tin oxide (ITO) nanohelix (NH) array is presented as a multifunctional electrode for bulk heterojunction organic solar cells for simultaneously improving light absorption and charge transport from the active region to the anode. It is shown that the ITO NH array, which is easily fabricated using an oblique‐angle‐deposition technique, acts as an effective antireflection coating as well as a light‐scattering layer, resulting in much enhanced light harvesting. Furthermore, the larger interfacial area between the electrode and the active layer, together with the enhanced carrier mobility through highly conductive ITO NH facilitate transport and collection of charge carriers. The optical and electrical improvements enabled by the ITO NH electrode result in a 10% increase in short‐circuit current density and power‐conversion efficiency of the solar cells.
Structural Changes of Gluten/Glycerol Plastics under Dry and Moist Conditions and during Tensile Tests (2016)

The structures of wheat gluten-based materials are greatly influenced by plasticizer content, moisture content, and external mechanical loading. In this study, the effects of moisture on the structure of wheat gluten (WG) plasticized by glycerol were investigated by using in situ small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS), mechanical tensile testing, and thermal analyses. The materials were processed with additives of ammonium hydroxide/salicylic acid or urea and conditioned at 0, 50, and 100% relative humidity (RH). In general, water showed similar effects on the WG structure and mechanical properties regardless of the type of additive. It was observed that the known hexagonal close-packed (HCP) structure in WG was present mainly under moist conditions and swelled with an increase in water content. The absorbed water molecules hydrated the protein chains at 50% RH and further led to the formation of a separate water/glycerol phase at 100% RH. An interesting feature was observed by in situ SAXS during tensile deformation; both the HCP structure and other protein aggregates packed more densely in both the tensile and transverse directions. It is interpreted as follows: “randomly oriented” chains were drawn out and stretched in the tensile direction, which squeezes the self-assembled structures together, similar to “tightening a knot”.
RhCMV serostatus and vaccine adjuvant impact immunogenicity of RhCMV/SIV vaccines (2020)

Rhesus cytomegalovirus (RhCMV) strain 68-1-vectored simian immunodeficiency virus (RhCMV/SIV) vaccines are associated with complete clearance of pathogenic SIV challenge virus, non-canonical major histocompatibility complex restriction, and absent antibody responses in recipients previously infected with wild-type RhCMV. This report presents the first investigation of RhCMV/SIV vaccines in RhCMV-seronegative macaques lacking anti-vector immunity. Fifty percent of rhesus macaques (RM) vaccinated with a combined RhCMV-Gag, -Env, and -Retanef (RTN) vaccine controlled pathogenic SIV challenge despite high peak viremia. However, kinetics of viral load control by vaccinated RM were considerably delayed compared to previous reports. Impact of a TLR5 agonist (flagellin; FliC) on vaccine efficacy and immunogenicity was also examined. An altered vaccine regimen containing an SIV Gag-FliC fusion antigen instead of Gag was significantly less immunogenic and resulted in reduced protection. Notably, RhCMV-Gag and RhCMV-Env vaccines elicited anti-Gag and anti-Env antibodies in RhCMV-seronegative RM, an unexpected contrast to vaccination of RhCMV-seropositive RM. These findings confirm that RhCMV-vectored SIV vaccines significantly protect against SIV pathogenesis. However, pre-existing vector immunity and a pro-inflammatory vaccine adjuvant may influence RhCMV/SIV vaccine immunogenicity and efficacy. Future investigation of the impact of pre-existing anti-vector immune responses on protective immunity conferred by this vaccine platform is warranted.
Cross-layer H.264 scalable video downstream delivery over WLANs (2010)

Thanks to its in-network drop-based adaptation capabilities, H.264 Scalable Video Coding is perceived as an effective approach for delivering video over networks characterized by sudden large bandwidth fluctuations, such as Wireless LANs. Performance may be boosted by the adoption of application-aware/cross-layer schedulers devised to intelligently drop video data units (NALUs), so that i) decoding dependencies are preserved, and ii) the quality perceived by the end users is maximized. In this paper, we provide a theoretical formulation of a QoE utility-optimal cross-layer scheduling problem for H.264 SVC downlink delivery over WLANs. We show that, because of the unique characteristics of the WLAN MAC operation, this problem significantly differs from related approaches proposed for scheduled wireless technologies, especially when the WLAN carries background traffic in the uplink direction. From these theoretical insights, we derive, design, implement and experimentally assess a simple practical scheduling algorithm, whose performance is very close to the optimal solution.
BIOLOGICAL INTERVENTION BASED ON CELL AND GENE THERAPY TO IMPROVE MUSCLE HEALING AFTER LACERATION (2000)

Muscle laceration is a challenging problem in traumatology and is common in sports injuries, with functional recovery remaining slow and incomplete. Even though muscles retain their ability to regenerate after injury, muscles' healing process after such injuries has been found to be very slow and often leads to incomplete muscle recovery. Growth factors may have a role in enhancing recovery. Our previous study showed that IGF-1, β-FGF and NGF can improve myoblast proliferation and differentiation in vitro. We then investigated whether the delivery of IGF-1 would improve muscle healing after injuries. We observed that muscle regeneration was enhanced in lacerated muscles treated with IGF-1 protein, which consequently led to an improvement in muscle healing. However, the rapid clearance and short biological half-lives of these proteins may have limited the success of this approach. We then investigated the efficiency of gene therapy based on adenovirus to deliver a stable expression of the growth factor IGF-1. Although a slight improvement in the healing process occurred in the muscle injected with adenovirus (AIGF), the combination of myoblast transplantation and gene therapy with the ex vivo approach further improved the healing process. The injection of normal myoblasts into the injured muscle led to the best improvement of muscle healing at two weeks post-injection. Implantation of normal minced muscle into mdx mice was also capable of improving muscle healing at 2–4 weeks post-implantation. These studies will further our understanding of muscle healing post-injury and help in the development of strategies to promote efficient muscle healing and complete functional recovery after common muscle injuries.
Rapid and easy protein staining for SDS‐PAGE using an intramolecular charge transfer‐based fluorescent reagent (2006)

High-performance staining for 1-D and 2-D SDS-PAGE was carried out using a novel protein-binding fluorophore (Dye 1), which noncovalently interacts with proteins and provides a fluorescence emission response to proteins by intramolecular charge transfer. In order to achieve the high-throughput analysis of proteins for SDS-PAGE, the general protocols for in-gel protein staining (SDS-PAGE, fixation, staining, washing, and detection) were simplified to produce an easy and rapid protocol (SDS-PAGE together with staining, washing, and detection). This method was performed by preparation of an electrophoresis buffer containing Dye 1 under optimum conditions, and by the binding of Dye 1 to proteins in the gel during the SDS-PAGE. As a result, this study required only 15 min for protein staining as a minimum time. On the other hand, it takes several hours for the general protein staining method, such as SYPRO Ruby staining (18 h) and CBB staining (105 min). Moreover, the protein-to-protein variation was low, and the detection limit was 7.0 ng/band of BSA (S/N = 3.0) in this method, which was as sensitive as the short-protocol silver staining methods. On the basis of these results, this rapid and easy protocol for SDS-PAGE using Dye 1 may be widely applicable and convenient for users in the various scientific and medical fields.
Alternative splicing of CD200 is regulated by an exonic splicing enhancer and SF2/ASF (2010)

CD200, a type I membrane glycoprotein, plays an important role in prevention of inflammatory disorders, graft rejection, autoimmune diseases and spontaneous fetal loss. It also regulates tumor immunity. A truncated CD200 (CD200(tr)) resulting from alternative splicing has been identified and characterized as a functional antagonist to full-length CD200. Thus, it is important to explore the mechanism(s) controlling alternative splicing of CD200. In this study, we identified an exonic splicing enhancer (ESE) located in exon 2, which is a putative binding site for a splicing regulatory protein SF2/ASF. Deletion or mutation of the ESE site decreased expression of the full-length CD200. Direct binding of SF2/ASF to the ESE site was confirmed by RNA electrophoretic mobility shift assay (EMSA). Knockdown of expression of SF2/ASF resulted in the same splicing pattern as seen after deletion or mutation of the ESE, whereas overexpression of SF2/ASF increased expression of the full-length CD200. In vivo studies showed that viral infection reversed the alternative splicing pattern of CD200 with increased expression of SF2/ASF and the full-length CD200. Taken together, our data suggest for the first time that SF2/ASF regulates the function of CD200 by controlling CD200 alternative splicing, through direct binding to an ESE located in exon 2 of CD200.
Primary Immunodeficiency Diseases: An Update on the Classification from the International Union of Immunological Societies Expert Committee for Primary Immunodeficiency (2014)

We report the updated classification of primary immunodeficiencies (PIDs) compiled by the Expert Committee of the International Union of Immunological Societies. In comparison to the previous version, more than 30 new gene defects are reported in this updated version. In addition, we have added a table of acquired defects that are phenocopies of PIDs. For each disorder, the key clinical and laboratory features are provided. This classification is the most up-to-date catalog of all known PIDs and acts as a current reference of the knowledge of these conditions and is an important aid for the molecular diagnosis of patients with these rare diseases.
A data parallel algorithm for ray tracing of heterogeneous databases (1992)

We describe a new data parallel algorithm for raytracing. Load balancing is achieved through the use of processor allocation, which continually remaps available resources. In this manner heterogeneous data bases are handled without the usual problems of low resource usage. The proposed approach adapts well to both extremes: a small number of rays and a large database; a large number of rays and a small database. The algorithm scales linearly---over a wide range---in the number of rays and available processors. We present an implementation on the Connection Machine CM2 system and provide timings. R&amp;apos;esum&amp;apos;e Cet article pr&amp;apos;esente un nouvel algorithme parall`ele pour le lancer de rayons. L&amp;apos;allocation des processeurs, qui distribue la tache aux resources disponibles, permet de garder une charge bien r&amp;apos;epartie. Ainsi &amp;apos;evitons nous les probl`emes usuels dus aux ressources de bas niveau tout en manipulant des structures de donn&amp;apos;ees h&amp;apos;et&amp;apos;erog`enes. Notre approche s&amp;apos;applique aussi bien `a un f...
DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters (2012)

This article introduces DoBISCUIT (Database of BIoSynthesis clusters CUrated and InTegrated, http://www.bio.nite.go.jp/pks/), a literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. Bacterial secondary metabolites often show pharmacologically important activities and can serve as lead compounds and/or candidates for drug development. Biosynthesis of each secondary metabolite is catalyzed by a number of enzymes, usually encoded by a gene cluster. Although many scientific papers describe such gene clusters, the gene information is not always described in a comprehensive manner and the related information is rarely integrated. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.
Endogenous Sterol Metabolites Regulate Growth of EGFR/KRAS-Dependent Tumors via LXR (2015)

Meiosis-activating sterols (MAS) are substrates of SC4MOL and NSDHL in the cholesterol pathway and are important for normal organismal development. Oncogenic transformation by epidermal growth factor receptor (EGFR) or RAS increases the demand for cholesterol, suggesting a possibility for metabolic interference. To test this idea in vivo, we ablated Nsdhl in adult keratinocytes expressing KRAS(G12D). Strikingly, Nsdhl inactivation antagonized the growth of skin tumors while having little effect on normal skin. Loss of Nsdhl induced the expression of ATP-binding cassette (ABC) transporters ABCA1 and ABCG1, reduced the expression of low-density lipoprotein receptor (LDLR), decreased intracellular cholesterol, and was dependent on the liver X receptor (LXR) α. Importantly, EGFR signaling opposed LXRα effects on cholesterol homeostasis, whereas an EGFR inhibitor synergized with LXRα agonists in killing cancer cells. Inhibition of SC4MOL or NSDHL, or activation of LXRα by sterol metabolites, can be an effective strategy against carcinomas with activated EGFR-KRAS signaling.
Impaired B Cell Development and Function in the Absence of IκBNS (2011)

IκBNS has been identified as a member of the IκB family of NF-κB inhibitors, which undergoes induction upon TCR signaling. Mice carrying a targeted gene disruption of IκBNS demonstrate dysregulation of cytokines in T cells, macrophages, and dendritic cells. IκBNS mediates both positive and negative gene regulation, depending on individual cell type and/or cytokine. In this study, we demonstrate an additional role for IκBNS in the B cell lineage. B cells from IκBNS knockout (KO) mice were impaired in proliferative responses to LPS and anti-CD40. IgM and IgG3 Igs were drastically reduced in the serum of IκBNS KO mice, although IκBNS KO B cells exhibited a higher level of surface IgM than that found in wild-type mice. Switching to IgG3 was significantly reduced in IκBNS KO B cells. The in vitro induction of plasma cell development demonstrated that progression to Ab-secreting cells was impaired in IκBNS KO B cells. In agreement with this finding, the number of Ab-secreting cells in the spleens of IκBNS KO mice was reduced and production of Ag-specific Igs was lower in IκBNS KO mice after influenza infection as compared with wild-type mice. Additionally, IκBNS KO mice lacked B1 B cells and exhibited a reduction in marginal zone B cells. Thus, IκBNS significantly impacts the development and functions of B cells and plasma cells.
Modular Multilevel Converter Circulating Current Control with Single Active Filter Module per Phase (2021)

Phase-legs of DC/AC modular multilevel converters (MMC, M2LC) transfer power from the DC input to the corresponding phase output terminal by means of a current that circulates through the DC input and the phase-leg. In addition to the load-dependent DC component required for the power transfer, this circulating current contains significant harmonics if no countermeasures are implemented. Prominently, a large second harmonic appears, essentially because each converter arm performs a single-phase power conversion. This results in higher RMS values of the arm currents and ultimately in higher-than-necessary losses. One option to mitigate these undesired harmonics and the associated losses extends each arm of the MMC by an active filter module that controls the circulating current by injecting a common-mode component into the arm voltage. In this paper, we propose a new variant of an MMC topology with such active filter modules. In contrast to the state of the art, the proposed realization shows lower realization effort: it uses only a single active filter module per MMC phase-leg instead of two, which corresponds to a reduced effort in terms of both, power hardware components and also control and communication electronics. Furthermore, a single active filter module can operate fully self-contained if desired, i.e., without an external communication interface, thus simplifying system integration.
One-dimensional thermonuclear burn computations for the Reversed-Field Pinch Reactor (RFPR) (1980)

Conceptual fusion reactor designs of the Reversed-Field Pinch Reactor (RFPR) have been based on profile-averaged zero-dimensional (point) plasma models. The plasma response/performance that has been predicted by the point plasma model is re-examined by a comprehensive one-dimensional (radial) burn code (RFPBRN) that has been developed and parametrically evaluated for the RFPR. The RFPR plasma parameters have been optimized and effects of turbulent transport and stability have been studied.
Acquired TET2 mutation in one patient with familial platelet disorder with predisposition to AML led to the development of pre‐leukaemic clone resulting in T2‐ALL and AML‐M0 (2016)

Familial platelet disorder with predisposition to acute myeloid leukaemia (FPD/AML) is characterized by germline RUNX1 mutations, thrombocytopaenia, platelet dysfunction and a risk of developing acute myeloid and in rare cases lymphoid T leukaemia. Here, we focus on a case of a man with a familial history of RUNX1<sup>R174Q</sup> mutation who developed at the age of 42 years a T2-ALL and, 2 years after remission, an AML-M0. Both AML-M0 and T2-ALL blast populations demonstrated a loss of 1p36.32-23 and 17q11.2 regions as well as other small deletions, clonal rearrangements of both TCRγ and TCRδ and a presence of 18 variants at a frequency of more than 40%. Additional variants were identified only in T2-ALL or in AML-M0 evoking the existence of a common original clone, which gave rise to subclonal populations. Next generation sequencing (NGS) performed on peripheral blood-derived CD34<sup>+</sup> cells 5 years prior to T2-ALL development revealed only the missense TET2<sup>P1962T</sup> mutation at a frequency of 1%, which increases to more than 40% in fully transformed leukaemic T2-ALL and AML-M0 clones. This result suggests that TET2<sup>P1962T</sup> mutation in association with germline RUNX1<sup>R174Q</sup> mutation leads to amplification of a haematopoietic clone susceptible to acquire other transforming alterations.
Multi-user Motion JPEG2000 over wireless LAN: Run-time performance-energy optimization with application-aware cross-layer scheduling (2006)

This paper introduces a video application-aware cross-layer framework for joint performance-energy optimization, considering the scenario of multiple users upstreaming real-time Motion JPEG2000 video streams to the access point of a WiFi wireless local area network and extends the PHY-MAC run-time cross-layer scheduling strategy that we introduced in (Mangharam et al., 2005; Pollin et al., 2005) to also consider congested network situations where video packets have to be dropped. We show that an optimal solution at PHY-MAC level can be highly suboptimal at application level, and then show that making the cross-layer framework application-aware through a prioritized dropping policy capitalizing on the inherent scalability of Motion JPEG2000 video streams leads to drastic average video quality improvements an inter-user quality variation reductions of as much as 10 dB PSNR, without affecting the overall energy consumption requirements.
Drug Design for G‐Protein‐Coupled Receptors by a Ligand‐Based NMR Method (2010)

A nonradioactive binding assay relying on NMR methods has been devised for a G-protein-coupled receptor; in addition the INPHARMA methods give access to the relative orientation of multiple ligands and supports ligand-based drug design (see picture of superimposed ligands). The method is fast and does not require any structural information from protein crystal structures.
Prophylactic strategies in recurrent vulvovaginal candidiasis: a 2-year study testing a phytonutrient vs itraconazole. (2013)

The aim of the present study was to assess the clinical efficacy of a one week/month treatment with a phytocompound with antimycotic properties (K-712, with following 100 mg composition: 10 mg of oleoresin from Pseudowintera colorata at 30 percent concentration in Polygodial together with trace amounts of Olea europea) in recurrent vulvo-vaginal candidiasis (RVVC), as compared to once a week treatment with an azole drug for 24 months follow up. This prospective randomized study involving 122 women (19 to 63 years old) with a history of proven episodes of RVVC in the prior 12 months. Patients were allocated in two treatment groups of 61 patients each and given A) Itraconazole 200 mg orally once a week or B) 1 tab twice a day of K-712 for one week/month. Each treatment schedule was well tolerated with 19 patients in the azole group complaining of transient mild symptoms (nausea, abdominal discomfort, unpleasant taste), while only 3 patients on K-712 reported slight dyspepsia. The number of relapses was significantly lower in the K-712-treated group as compared to the itraconazole-group (22 vs 39, p less than 0.05). Moreover, the former group showed a significantly decreased number of cases resistant or dose-dependent susceptible as compared to group A (p less than 0.05 vs itraconazole) and the same occurred for the occurrence of non-albicans species (group A 64.1 percent vs group B 31.8 percent, p less than 0.05). The overall mycological cure at the end of the 2-year study showed a comparable benefit between the two groups. From these data it appears that the present antifungal phytonutrient is equally effective as itraconazole in the overall treatment of RVVC over a 2-year follow-up, but yielding a significantly better prophylactic effect and also maintenance benefit with lower relapse rate, antifungal susceptibility and growth of azole-resistant species.
Simulation and Experimental Verification of an Argon DC Glow Discharge (2021)

A coordinated experimental-simulation study was carried out to explore the relationship between plasma conditions and ion angular energy distributions incident on a DC glow discharge cathode. Langmuir probe measurements of the Electron Energy Distribution Functions (EEDF) validated a COMSOL simulation’s accuracy which confirmed the proper methodology for reproducing discharge dynamics. 1 The simulation was a coupling between COMSOL’s Plasma module and Boltzmann Equation, Two-Term Approximation module allowing for accurate calculations of the Townsend coefficients. Proper Townsend coefficients are necessary to represent the kinetics of DC discharges with low ionization fractions and species mobility that are highly dependent on the electric field, e.g., ions transiting the plasma sheath. The EEDFs were measured along the cathode dark space and negative glow regions using the Druyvesteyn method. 2 After the trend of EEDFs were validated, the model was expanded to extract ion angular energy distributions in conditions where measuring plasma properties became no longer feasible.