gebhart/patrepeval huggingface dataset:
Synthesis of a gene for sensory rhodopsin I and its functional expression in Halobacterium halobium. (1993)

We have designed, synthesized, and expressed in Halobacterium halobium a gene encoding sensory rhodopsin I (SR-I). The gene has been optimized for cassette mutagenesis by incorporating 30 unique restriction sites with uniform spacing throughout the 720-bp coding region. For expression, the coding region was placed downstream of the promoter and translation initiation region of the bacterioopsin gene on a selectable vector. This construct encodes SR-I with an extended N terminus that includes the 13-amino acid leader sequence and the 8-amino acid N terminus of bacterioopsin. To obtain a SR-I- H. halobium strain for expressing the synthetic gene, we used homologous recombination to delete the chromosomal gene encoding SR-I, sopI. The deletion strain was transformed with the synthetic sopI expression vector. Using antibody directed against the C-terminal region of SR-I, we detected in transformant membranes a protein with the electrophoretic mobility expected for SR-I with a processed N-terminal extension. The synthetic gene product was functionally identical to SR-I. Its flash-induced absorption difference spectrum and photochemical reaction cycle in membrane envelope vesicles were characteristic of SR-I. The protein fully restored phototaxis responses in the deletion strain.
Ultra-Low Power Stationary Plasma Thruster (2005)

This study summarizes the first Slovak experience with vinflunine therapy. Our data confirmed the efficacy of vinflunine and its acceptable toxicity in the treatment of patients with advanced urothelial cancer previously treated with a platinum-based regimen.Key words: advanced urothelial cancer - vinflunine - progression-free survival - overall survival - side effects.
Identification and quantification of complement regulator CD46 on normal human tissues. (1993)

CD46 is a cell-surface regulatory molecule that prevents lysis of autologous human cells by activated complement. It has been well characterized on leucocytes, reproductive cells and various cultured cell lines and is considered to be ubiquitously expressed. We now extend these analyses and describe CD46 in a variety of different human tissues. Strong expression was observed by immunohistology on epithelial cells lining exocrine ducts and glands, such as salivary gland and pancreas and on kidney tubules and glomerular epithelium. Quantitative tissue expression was measured by radioimmunoassay and confirmed histological observations. Thus, CD46 is highly expressed on cells in contact with extracellular fluids thought not to contain large quantities of complement but which may still be subjected to complement attack thereby necessitating the presence of complement regulators to prevent non-specific destruction of cells.
IRF3 signaling pathway serves an important role in poly(I:C)-induced procollagen reduction in human skin fibroblasts (2017)

Pattern recognition receptors (PRRs) are part of the immune system. They can recognize pathogen‑associated molecular patterns (PAMPs). Toll‑like receptors (TLRs) and retinoic acid‑inducible gene 1 (RIG‑1)‑like receptors (RLRs) are 2 types of PRR in the innate immune system. Double‑stranded RNA (dsRNA) can exist as a PAMP, including dsRNA viruses. dsRNA is known as a ligand not only for TLR3 but also for RLRs, including melanoma differentiation‑associated gene 5 and RIG‑1. Collagen is the main structural protein in the extracellular space in the skin. Recently, it was reported that treatment of a synthetic dsRNA, poly(I:C), decreases procollagen expression in skin fibroblasts. However, signaling pathways involved in this process have not yet been fully elucidated. The present study further explored the underlying signaling pathways involved in the processes. It was demonstrated by western blotting that treatment of poly(I:C), but not another PAMP, Pam3CSK4, inhibited procollagen expression in cultured human skin fibroblasts. Treatment of poly(I:C)and Pam3CSK4 induced activation of the mitogen‑activated protein kinases and the nuclear factor‑κB pathways. However, only poly(I:C), but not Pam3CSK4, induced the activation of the interferon regulatory factor 3 (IRF3) pathway. By using specific inhibitors, it was demonstrated that inhibition of IRF3 pathway relieved poly(I:C)‑induced procollagen reduction. In conclusion, IRF3 signaling pathway serves an important role in poly(I:C)‑induced procollagen reduction in skin fibroblasts. This suggests that the IRF3 signaling pathway may be a key target for collagen regulation in the skin.
Leak detection and location in gas pipelines (1988)

The paper describes a new method for detecting and locating leaks in long pipelines, based on an extended Kalman filter for the nonlinear Distributed Parameter (DP) system representing gas flow in pipes. Artificial leak states at predefined positions along the pipeline are included in the filter model, and relationships to estimate the actual leak position are derived. Simulation results are presented to assess the method.
High Toughness in Ultralow Density Graphene Oxide Foam (2017)

Here, the scalable synthesis of low‐density 3D macroscopic structure of graphene oxide (GO) interconnected with polydimethylsiloxane (PDMS) is reported. A controlled amount of PDMS is infused into the freeze‐dried foam to result into a very rigid structure with improved mechanical properties, such as tensile plasticity and toughness. The PDMS wets the graphene oxide sheets and acts like glue between the 2D sheets. Molecular dynamics simulations are used to further elucidate the mechanisms of the interactions of graphene oxide layers with PDMS. The ability of using the interconnecting graphene oxide foam as an effective oil–water separator and stable insulating behavior to elevated temperatures are further demonstrated. The structural rigidity of the sample is also tested using laser impact and compared with GO foam.
Catalytic Efficiency of Primary α-Amino Amides as Multifunctional Organocatalysts in Recent Asymmetric Organic Transformations (2022)

Chiral primary α-amino amides, consisting of an adjacent enamine bonding site (Bronsted base site), a hydrogen bonding site (Bronsted acid site), and flexible bulky substituent groups to modify the steric factor, are proving to be extremely valuable bifunctional organocatalysts for a wide range of asymmetric organic transformations. Primary α-amino amides are less expensive alternatives to other primary amino organocatalysts, such as chiral diamines and cinchona-alkaloid-derived primary amines, as they are easy to synthesize, air-stable, and allow for the incorporation of a variety of functional groups. In recent years, we have demonstrated the catalytic use of simple primary α-amino amides and their derivatives as organocatalysts for the aldol reaction, Strecker reaction, Michael tandem reaction, allylation of aldehydes, reduction of N-Aryl mines, opening of epoxides, hydrosilylation, asymmetric hydrogen transfer, and N-specific nitrosobenzene reaction with aldehydes.
Evolutionary assessment of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in citrus relatives with a specific focus on flowering (2023)

Phase transition and floral induction in citrus requires several years of juvenility after germination. Such a long period of juvenility has been a major hindrance to its genetic improvement program. Studies have shown that miR156 along with its downstream genes SQUAMOSA PROMOTER BINDING PROTEINS (SBP) and SBP-LIKE (SPL) mediate the phase transition and floral induction process in plants. Our current study has systematically analyzed SPLs in 15 different citrus-related species, systematically annotated them based on their close homology to their respective Arabidopsis orthologs, and confirmed the functional attributes of the selected members in floral precocity. The majority of the species harbored 15 SPLs. Their cis-element assessment suggested the involvement of the SPLs in diverse developmental and physiological processes in response to different biotic and abiotic cues. Among all, SPL5, SPL9, and SPL11 stood out as consistently differentially expressed SPLs in the adult and young tissues of different citrus-related species. Independent overexpression of their F. hindsii orthologs (FhSPL5, FhSPL9, and FhSPL11) brought an enhanced expression of endogenous FLOWERING LOCUS T leading to the significantly precocious flowering in transgenic Arabidopsis lines. Future study of the genes in the citrus plant itself is expected to conclude the assessments made in the current study.
Circumventing the Phonon Bottleneck by Multiphonon-Mediated Hot Exciton Cooling at the Nanoscale (2023)

In semiconductor materials, hot exciton cooling is the process by which highly excited carriers nonradiatively relax to form a band edge exciton. While cooling plays an important role in determining the thermal losses and quantum yield of a system, the timescales and mechanism of cooling are not well understood in confined semiconductor nanocrystals (NCs). A mismatch between electronic energy gaps and phonon frequencies in NCs has led to the hypothesis of a phonon bottleneck, in which cooling would be extremely slow, while enhanced electron-hole interactions in NCs have been used to explain cooling that would occur on ultrafast timescales. Here, we develop an atomistic approach for describing phonon-mediated exciton dynamics, and we use it to simulate hot exciton cooling in NCs of experimentally relevant sizes. Our framework includes electron-hole correlations as well as multiphonon processes, both of which are necessary to accurately describe the cooling process. We find that cooling occurs on timescales of tens of femtoseconds in CdSe cores, in agreement with experimental measurements, through a cascade of relaxation events that are mediated by efficient multiphonon emission. Cooling timescales increase with increasing NC size due to decreased exciton-phonon coupling (EXPC), and they are an order of magnitude larger in CdSe-CdS core-shell NCs because of reduced EXPC to low- and mid-frequency acoustic modes.
Agile Prototypenentwicklung und -evaluation mit SMPL++ (2007)

Der rapide technische Fortschritt führt in immer kürzeren Abständen zu Veränderungen der Rollen- und Funktionsteilung zwischen Mensch und Technik. Im Kraftfahrzeug haben im Zuge dieser Entwicklung immer mehr Fahrerassistenzsysteme Einzug gehalten. Nachdem erste Systeme eine relativ einfache Funktionsweise besaßen (wie zum Beispiel ABS), nimmt zur Zeit die Komplexität solcher Assistenzsysteme mit Eingriffen in die Längs- und Querführung (z.B. ACC, LKAS) deutlich zu. Eine Art Wettlauf der Fahrzeughersteller zu immer innovativeren und stärker eingreifenden Fahrerassistenzsysteme steht möglicherweise kurz bevor. In der Luftfahrt hat eine vergleichbare Entwicklung hin zur Automation bereits früher eingesetzt und zu Sicherheits- und Komfortgewinnen, gleichzeitig aber auch zu neuen Problemen gerade im Zusammenspiel zwischen Mensch und Automation geführt. Nur wenn diese Probleme von Anfang an adressiert werden, hat die Entwicklung der Automation im Kraftfahrzeug überhaupt eine Chance, Sicherheit, Effizienz und Komfort zu erhöhen. &#13;\n&#13;\nZentrale Bedeutung bei der Vermeidung dieser Automationsprobleme kommt dabei Methoden wie der agilen Prototypenentwicklung in Verbindung mit integriertem Testen zu, mit dem verschiedene Auslegungen neuer Systeme bereits in einer frühen Entwicklungsphase gestaltet, analysiert und evaluiert werden können. &#13;\n&#13;\nDieser Beitrag umfasst: &#13;\n&#13;\neine Einführung in agile Software- und Prototypenentwicklung &#13;\nMethodiken der agilen Prototypenentwicklung wie der Wizard-Of-Oz-Technik, dem Theatersystem etc. &#13;\nEinblicke in das Straightforward Modular Prototyping Laboratory (SMPLab) am Institut für Verkehrsfürung und Fahrzeugsteuerung beim DLR Braunschweig &#13;\nEinblicke in den Softwareansatz SMPL++ &#13;\n
Biochemical analysis of actin in crane-fly gonial cells: evidence for actin in spermatocytes and spermatids--but not sperm. (1980)

A biochemical assay employing DNase-I affinity chromatography, two-dimensional peptide analysis and SDS polyacrylamide gel electrophoresis was used to isolate, identify, and assess the amount of actin from gonial cells of the crane fly, Nephrotoma suturalis. Based on the analysis of cell homogenates under conditions in which all cellular actin is converted to the monomeric DNase-binding form, actin comprises approximately 1% of the total protein in homogenates of spermatocytes and spermatids. SDS gel analysis of mature sperm reveals no polypeptides with a molecular weight similar to that of actin. Under conditions that preserve native supramolecular states of actin, approximately 80% of the spermatocyte actin is in a sedimentable form whereas only approximately 30% of the spermatid actin is sedimentable. These differences could be meaningful with regard to strutural changes that occur during spermiogenesis. A comparative analysis of two-dimensional peptide maps of several radioiodinated actins reveals similarities among spermatocyte, spermatid, and human erythrocyte actins. The results suggest the general applicability of this approach to other cell types that contain limited amounts of actin.
Stacking fault and defects in single domain multilayered hexagonal boron nitride (2017)

Two dimensional materials like graphene, transition metal dichalcogenides, and hexagonal boron nitride (h-BN) have attracted a keen interest over the past few years due to their possible integration in the next generation of nano-components. Here, we used high resolution X-ray photoemission spectroscopy and near-edge X-ray absorption fine structure (NEXAFS) to perform a complete study of stacking configuration and identify sp3 crystal deformations of a single domain h-BN crystal. The AA′ stacking was found to best reproduce features in the experimental B and N K-edges. The NEXAFS also shows that the splitting of the 1s to π* peak in the B K-edge, recently predicted by density functional theory, may be accounted for by the presence of AB′ stacking faults. The presence of this stacking fault has, as a result, the introduction of point defects in the crystal such as boron atoms in a pyramidal or sp3 configuration. Interstitial nitrogen defects are also present in the crystal forming a N-N pair as expected for a p-type h-BN crystal.
Die Suche nach neuen umweltfreundlichen chemischen Prozessen (1999)

Risiken bei chemisch-industriellen Verfahren minimieren und mögliche Gefahrstoffe bei der Produktion vermeiden – dies sind die Ziele umweltfreundlicher chemischer Prozesse. Dabei können diese auch einen ökonomischen Vorteil bieten. Wie dieser Ansatz zu einem umweltfreundlicheren chemischen Verfahren führen kann, demonstriert der Vergleich einer neuartigen, beinahe ideal atomökonomisch verlaufenden Oxidation zu Adipinsäure 1 (siehe Schema) mit deren herkömmlicher Synthese. [W] = Wolfram-Katalysator.
Dual-Band Antenna Array for 5.9 GHz DSRC and 28 GHz 5G Vehicle to Vehicle communication (2020)

The Dedicated Short Range Communications (DSRC) band (5.85-5.925 GHz) allocated for vehicle-to-vehicle (V2V) communication provides limited opportunities for high speed data transfer. Alternatively, FCC plans to allocate millimeter-wave spectrum for 5G V2V communication. In this paper, we present a novel dual-band dual linearly-polarized antenna array for both DSRC and 28 GHz communications. For each band, we optimized antenna gain and number of elements to maximize range and data rate. The designed array has dual linear polarization and is fed with a simple quarter wave transformer. Due to large available connector's size, a Wilkinson power divider is designed to combine adjacent elements. Infinite array simulation show that the array is well matched from 5.85 to 6.48 GHz, and from 17.29 to 29 GHz. The realized gain at both frequency bands is near-theoretical.
Translation and Validation of the Dutch Version of the New Knee Society Knee Scoring System (2018)

Background:Recently a new version of the Knee Society Knee Scoring System has been developed, adapted to the lifestyle and activities of contemporary patients with a Total Knee Arthroplasty (TKA). It is subdivided into 4 domains including an Objective Knee Score, a Satisfaction Score, an Expectations Score and a Functional Activity Score. Before this scale can be used in non-English speaking populations, it has to be translated and validated for specific populations. The aim of this study was to translate and validate the New Knee Society Knee Scoring System (new KSS) for Dutch speaking populations.Materials and Methods:A Dutch translation of the New KSS was established using a forward-backward translation protocol. 137 patients undergoing TKA were asked to complete the Dutch translation of the New KSS as well as the Dutch WOMAC, Dutch KOOS and the Dutch SF12. To determine the test-retest reliability, 53 patients were asked to fill out a second questionnaire with one-week interval. We tested the test-rete...
Data from Capecitabine Efficacy Is Correlated with TYMP and RB1 Expression in PDX Established from Triple-Negative Breast Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Triple-negative breast cancer (TNBC) patients with residual disease after neoadjuvant chemotherapy have a poor outcome. We developed patient-derived xenografts (PDX) from residual tumors to identify efficient chemotherapies and predictive biomarkers in a context of resistance to anthracyclines- and taxanes-based treatments.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; PDX were established from residual tumors of primary breast cancer patients treated in neoadjuvant setting. TNBC PDX were treated by anthracyclines, taxanes, platins, and capecitabine. Predictive biomarkers were identified by transcriptomic and immunohistologic analysis. Downregulation of &lt;i&gt;RB1&lt;/i&gt; was performed by siRNA in a cell line established from a PDX.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Residual TNBC PDX were characterized by a high tumor take, a short latency, and a poor prognosis of the corresponding patients. With the exception of BRCA1/2-mutated models, residual PDX were resistant to anthracyclines, taxanes, and platins. Capecitabine, the oral prodrug of 5-FU, was highly efficient in 60% of PDX, with two models showing complete responses. Prior treatment of a responder PDX with 5-FU increased expression of thymidylate synthase and decreased efficacy of capecitabine. Transcriptomic and IHC analyses of 32 TNBC PDX, including both residual tumors and treatment-naïve derived tumors, identified RB1 and TYMP proteins as predictive biomarkers for capecitabine response. Finally, &lt;i&gt;RB1&lt;/i&gt; knockdown in a cell line established from a capecitabine-responder PDX decreased sensitivity to 5-FU treatment.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We identified capecitabine as efficient chemotherapy in TNBC PDX models established from residual disease and resistant to anthracyclines, taxanes, and platins. RB1 positivity and high expression of TYMP were significantly associated with capecitabine response. &lt;i&gt;Clin Cancer Res; 24(11); 2605–15. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
In vitro differentiation of leukemic cells to eosinophils in the presence of interleukin-5 in two cases of acute myeloid leukemia with the translocation (8;21)(q22;q22) (1990)

We demonstrated the significant eosinophilic growth of leukemic cells in the presence of interleukin-5 (IL-5) in 2 of 15 cases of acute myeloid leukemia. These two cases were M2 (FAB classification) with the translocation (8;21)(q22; q22). Bone marrow examination revealed the rather high percentages (6% and 9%) of atypical eosinophils in the total nucleated bone marrow cells in these two cases. In the remaining 13 cases, eosinophils were less than 2% in the nucleated bone marrow cells. In the methylcellulose culture system, 142 +/- 18 or 54 +/- 2 colonies were formed by 5 x 10(4) mononuclear cells in the presence of IL-5 in these two cases. These colonies mainly comprised mature eosinophils. Eosinophils were confirmed by Biebrich scarlet staining and electron microscopic examination using a specific lectin binding assay. The eosinophilic differentiation and proliferation of leukemic cells were also observed in the liquid culture system. It was shown that eosinophils observed in both systems were derived from leukemic cells using the chromosomal marker of leukemic cells, t(8;21). Leukemic cells also differentiated to neutrophils or both neutrophils and eosinophils in response to granulocyte colony-stimulating factor or interleukin-3, respectively, but did not respond noticeably to granulocyte-macrophage colony-stimulating factor. Although IL-5 acts on normal eosinophil committed precursors as a lineage-specific growth factor, at least some leukemic cells reacted to IL-5 and could proliferate and differentiate along eosinophilic pathway. Our findings suggest that atypical eosinophils observed in the bone marrow were derived from the leukemic clone in two cases of AML.
Two-stage query segmentation for information retrieval (2009)

Modeling term dependence has been shown to have a significant positive impact on retrieval. Current models, however, use sequential term dependencies, leading to an increased query latency, especially for long queries. In this paper, we examine two query segmentation models that reduce the number of dependencies. We find that two-stage segmentation based on both query syntactic structure and external information sources such as query logs, attains retrieval performance comparable to the sequential dependence model, while achieving a 50% reduction in query latency.
Treatment Of Joint Pain In Crohn’s Patients With Budesonide Controlled Ileal Release§ (2000)

1. Joint pain is a frequent manifestation of Crohn's disease. Budesonide controlled ileal release (CIR) is a predominantly topically acting glucocorticosteroid, which is effective in treating active ileal or ileocaecal Crohn's disease. 2. Therefore, it was of interest to study the effect of this predominantly topically acting therapy on the treatment of an extraintestinal symptom of Crohn's disease by analysing data collected from budesonide CIR (Entocort; Astra Draco AB, Lund, Sweden) trials. 3. Three large studies of budesonide CIR treatment in active Crohn's disease provided a reliable source of clinical data. Of the 611 patients treated in the prospective double-blind controlled trials, 291 had joint pain (arthritis/arthralgia) at entry, which was recorded as part of the Crohn's Disease Activity Index. Statistical analysis was based on all patients treated, provided that the patient had joint pain at the start of treatment. 4. Daily oral budesonide CIR (9mg) resulted in clinical remission of joint pain in 74% (95% confidence intervals (CI) 67-82%) of patients. This outcome was nearly twice as good as placebo (41%; 95% CI 34-57%) and as good as the outcome effected by daily oral prednisolone (40mg; 72%; 95% CI 60-84%). The favourable response to budesonide CIR (9 mg) did not correlate with glucocorticosteroid-associated side effects or with adrenal suppression, which were half those in the prednisolone (40 mg/day) group. 5. The favourable outcome may relate to restitution of normal intestinal immune function.