gebhart/patrepeval huggingface dataset:
Large‐scale species delimitation method for hyperdiverse groups (2012)

Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell-based PSHs can be arduous. A four-pronged approach was employed to generate robust species hypotheses of a 1000 specimen South-West Pacific Turridae data set in which: (i) analysis of COI DNA Barcode gene is coupled with (ii) species delimitation tools GMYC (General Mixed Yule Coalescence Method) and ABGD (Automatic Barcode Gap Discovery) to propose PSHs that are then (iii) visualized using Klee diagrams and (iv) evaluated with additional evidence, such as nuclear gene rRNA 28S, morphological characters, geographical and bathymetrical distribution to determine conclusive secondary species hypotheses (SSHs). The integrative taxonomy approach applied identified 87 Turridae species, more than doubling the amount previously known in the Gemmula genus. In contrast to a predominantly shell-based morphological approach, which over the last 30 years proposed only 13 new species names for the Turridae genus Gemmula, the integrative approach described here identified 27 novel species hypotheses not linked to available species names in the literature. The formalized strategy applied here outlines an effective and reproducible protocol for large-scale species delimitation of hyperdiverse groups.
Photomorphogenic development of the Arabidopsisshy2–1D mutation and its interaction with phytochromes in darkness (1998)

We previously reported a photomorphogenic mutation of Arabidopsis thaliana, shy2-1D, as a dominant suppressor of a hy2 mutation. Here, we report that shy2-1D confers various photo-responsive phenotypes in darkness and the dark phenotypes of the mutant are affected by phytochrome deficiency. Dark-grown seedlings of the mutant developed several photomorphogenic characteristics such as short hypocotyls, cotyledon expansion and opening, and partial differentiation of plastids. When grown further in darkness, the mutant plant underwent most of the developmental stages of a light-grown wild-type plant, including development of foliar leaves, an inflorescence stem with cauline leaves, and floral organs. In addition, two light-inducible genes, the nuclear-encoded CAB and the plastid-encoded PSBA genes, were highly expressed in the dark-grown mutant seedlings. Furthermore, reduced gravitropism, a phytochrome-modulated response, was observed in the mutant hypocotyl in darkness. Thus, shy2-1D is one of the most pleiotropic photomorphogenic mutations identified so far. The results indicate that SHY2 may be a key component regulating photomorphogenesis in Arabidopsis. Surprisingly, double mutants of the shy2-1D mutant with the phytochrome-deficient mutants hy2, hy3(phyB-1) and fre1-1(phyA-201) showed reduced photomorphogenic response in darkness with a longer hypocotyl, a longer inflorescence stem, and a lower level expression of the CAB gene than the shy2-1D single mutant. These results showed that phytochromes function in darkness in the shy2-1D mutant background. The implications of these results are discussed.
Development and characterisation of novel cross-linked bio-elastomeric materials (2008)

Recombinantly-engineered elastin-like polypeptides (ELPs) possess many of the favourable attributes of the native elastin protein, making them an attractive option for designing biomaterials for tissue-engineering applications. The focus of this study was to synthesize and characterise the bulk material properties of two ELP sequences, ELP2 and ELP4, cross-linked with lysine diisocyanate (LDI). The two distinct ELPs consist of repeating hydrophobic and hydrophilic cross-linking domains in a block co-polymer structure, however, differ by the number of respective domains. Depending on the conditions sets for the cross-linking reactions, two different ELP-based materials were synthesized: a gel-like relatively non-porous material and a porous foam-like material, from both ELP sequences. The physical material properties were characterised by scanning electron microscopy, compression testing, differential calorimetry analysis and swelling analysis. The bulk material properties were found to vary depending on the ELP sequence investigated. ELP gels were also found to have a more dense solidified morphology, lower compressive moduli, higher melting temperature and greater swelling capacity than the porous ELP foams. These novel cross-linked bio-elastomeric materials show promising properties for soft tissue replacement, particularly in load-bearing applications.
The rare sugar N-acetylated viosamine is a major component of Mimivirus fibers (2017)

The giant virus Mimivirus encodes an autonomous glycosylation system that is thought to be responsible for the formation of complex and unusual glycans composing the fibers surrounding its icosahedral capsid, including the dideoxyhexose viosamine. Previous studies have identified a gene cluster in the virus genome, encoding enzymes involved in nucleotide-sugar production and glycan formation, but the functional characterization of these enzymes and the full identification of the glycans found in viral fibers remain incomplete. Because viosamine is typically found in acylated forms, we suspected that one of the genes might encode an acyltransferase, providing directions to our functional annotations. Bioinformatic analyses indicated that the L142 protein contains an N-terminal acyltransferase domain and a predicted C-terminal glycosyltransferase. Sequence analysis of the structural model of the L142 N-terminal domain indicated significant homology with some characterized sugar acetyltransferases that modify the C-4 amino group in the bacillosamine or perosamine biosynthetic pathways. Using mass spectrometry and NMR analyses, we confirmed that the L142 N-terminal domain is a sugar acetyltransferase, catalyzing the transfer of an acetyl moiety from acetyl-CoA to the C-4 amino group of UDP-d-viosamine. The presence of acetylated viosamine <i>in vivo</i> has also been confirmed on the glycosylated viral fibers, using GC-MS and NMR. This study represents the first report of a virally encoded sugar acetyltransferase.
Control of Linear Servo Carts with Integral-Based Disturbance Rejection (2022)

This paper describes a system designed for linear servo cart systems that employs an integral-based Linear Active Disturbance Rejection Control (ILADRC) scheme to detect and respond to disturbances. The upgrade in this control technique provides extensive immunity to uncertainties, attenuation, internal disturbances, and external sources of noise. The fundamental technology base of LADRC is Extended State Observer (ESO). LADRC, when combined with Integral action, becomes a hybrid control technique, namely ILADRC. Setpoint tracking is based on Bode’s Ideal Transfer Function (BITF) in this proposed ILADRC technique. This proves to be a very robust and appropriate pole placement scheme. The proposed LSC system has experimented with the hybrid ILADRC technique plotted the results. From the results, it is evident that the proposed ILADRC scheme enhances the robustness of the LSC system with remarkable disturbance rejection. Furthermore, the results of a linear quadratic regulator (LQR) and ILADRC schemes are comparatively analyzed. This analysis deduced the improved performance of ILADRC over the LQR control scheme.
Full range active AC Filter with multilevel IGBT converter for transmission and distribution systems (2008)

The first active AC filter at an HVDC station was installed by Siemens in 1998 in the HVDC Converter Station of Tjele, in Denmark as a demonstration project. This active filter used a 0.6 MVA IGBT converter. This paper introduces the new full range active AC filter developed as a new standard product by the same company, four of them were commissioned at the converter stations of the Neptune Regional Transmission System USA in 2007. These active filters have a 22 MVA multilevel IGBT converter and open new possibilities for harmonic mitigation at HVDC stations but also in other AC applications where such ratings are required.
Nonvolatile memristor memory (2009)

The search for new nonvolatile universal memories is propelled by the need for pushing power-efficient nanocomputing to the next higher level. As a potential contender for the next-generation memory technology of choice, the recently found "the missing fourth circuit element", memristor, has drawn a great deal of research interests. In this paper, we characterize the fundamental electrical properties of memristor devices by encapsulating them into a set of compact closed-form expressions. Our derivations provide valuable design insights and allow a deeper understanding of key design implications of memristor-based memories. In particular, we investigate the design of read and write circuits and analyze data integrity and noise-tolerance issues.
Predicting plasma protein binding of drugs--revisited. (2004)

Plasma protein binding of drugs has been studied for almost 100 years, but despite the accumulation of large amounts of data, the accurate prediction of this ADME parameter continues to be problematic. This review outlines recent efforts on the development of prediction tools for plasma protein binding of drugs, specifically human serum albumin, in the context of its relevance and its influencing factors. The issue of why it is difficult to achieve prediction of sufficient quality for a diverse dataset will also be considered.
Transferable Multi-Domain State Generator for Task-Oriented Dialogue Systems (2019)

Over-dependence on domain ontology and lack of knowledge sharing across domains are two practical and yet less studied problems of dialogue state tracking. Existing approaches generally fall short in tracking unknown slot values during inference and often have difficulties in adapting to new domains. In this paper, we propose a Transferable Dialogue State Generator (TRADE) that generates dialogue states from utterances using a copy mechanism, facilitating knowledge transfer when predicting (domain, slot, value) triplets not encountered during training. Our model is composed of an utterance encoder, a slot gate, and a state generator, which are shared across domains. Empirical results demonstrate that TRADE achieves state-of-the-art joint goal accuracy of 48.62% for the five domains of MultiWOZ, a human-human dialogue dataset. In addition, we show its transferring ability by simulating zero-shot and few-shot dialogue state tracking for unseen domains. TRADE achieves 60.58% joint goal accuracy in one of the zero-shot domains, and is able to adapt to few-shot cases without forgetting already trained domains.
A Phase II Trial of Oxaliplatin and Trastuzumab in the Treatment of HER2-Positive Metastatic Breast Cancer (2010)

We investigated the feasibility/efficacy of oxaliplatin in combination with trastuzumab as first-/second-line treatment of HER2-positive metastatic breast cancer (MBC). Patients received oxaliplatin/trastuzumab every 21 days and were evaluated every 6 weeks using RECIST criteria. The study closed early due to slow accrual. Twenty-five patients were evaluable; of these, 5 (20%) had objective responses to oxaliplatin/trastuzumab. Therapy was well tolerated (no grade-4 and gastrointestinal grade-3 toxicity in 4% of patients), but had only modest activity (median time-to-progression 1.8 months). Substitution of oxaliplatin for cisplatin or carboplatin, in combination with trastuzumab, does not appear to improve first-/second-line therapy in HER2-positive MBC.
Thermal testing of the proposed HUD energy efficiency standard for new manufactured homes (1992)

Thermal testing of two manufactured homes was performed at the National Renewable Energy Laboratory`s (NREL`s) Collaborative Manufactured Buildings Facility for Energy Research and Testing (CMFERT) environmental enclosure in the winter and spring of 1991. The primary objective of the study was to directly measure the thermal performance of the two homes, each built according to a proposed new US Department of Housing and Urban Development (HUD) standard. Secondary objectives were to test the accuracy of an accompanying compliance calculation method and to help manufacturers find cost-effective ways to meet the new standard. Both homes performed within the standard without major design or production line modifications. Their performance fell within 8% of predictions based on the new draft HUD calculation manual; however, models with minimum window area were selected by the manufacturer. Models with more typical window area would have required substantive design changes to meet the standard. Several other tests were also performed on the homes by both NREL and the Florida Solar Energy Center (FSEC) to uncover potential thermal anomalies and to explore the degradation in thermal performance that might occur because of (a) penetrations in the rodent barrier from field hookups and repairs, (b) closing of interior doors with and without operation of the furnace blower, and (c) exposure to winds.
Thermomechanical Mismatch in Ceramic‐Fiber‐Reinforced Glass‐Ceramic Composites (1987)

The thermomechanical relationship between mullite and a lithium aluminosilicate (LAS) glass‐ceramic has been studied by a technique of bimaterial dilatometry. The viscoelastic behavior of LAS was found to result in a temperature T rvsl below the glass‐transformation temperature T g at which the interfacial stresses between the materials undergo a reversal in sign. The effect of T rvsl on the high‐temperature mechanical properties of mullite or SiC fiber‐reinforced glass‐ceramic composites is discussed. It is suggested that fiber clamping by the matrix at temperatures between T rvsl and T g contributes to the brittle, high‐temperature behavior of such composites.
Data from Transcriptional Programs following Genetic Alterations in <i>p53</i>, <i>INK4A</i>, and <i>H-Ras</i> Genes along Defined Stages of Malignant Transformation (2023)

&lt;div&gt;Abstract&lt;p&gt;The difficulty to dissect a complex phenotype of established malignant cells to several critical transcriptional programs greatly impends our understanding of the malignant transformation. The genetic elements required to transform some primary human cells to a tumorigenic state were described in several recent studies. We took the advantage of the global genomic profiling approach and tried to go one step further in the dissection of the transformation network. We sought to identify the genetic signatures and key target genes, which underlie the genetic alterations in &lt;i&gt;p53&lt;/i&gt;, &lt;i&gt;Ras&lt;/i&gt;, &lt;i&gt;INK4A&lt;/i&gt; locus, and &lt;i&gt;telomerase&lt;/i&gt;, introduced in a stepwise manner into primary human fibroblasts. Here, we show that these are the minimally required genetic alterations for sarcomagenesis &lt;i&gt;in vivo&lt;/i&gt;. A genome-wide expression profiling identified distinct genetic signatures corresponding to the genetic alterations listed above. Most importantly, unique transformation hallmarks, such as differentiation block, aberrant mitotic progression, increased angiogenesis, and invasiveness, were identified and coupled with genetic signatures assigned for the genetic alterations in the &lt;i&gt;p53&lt;/i&gt;, &lt;i&gt;INK4A&lt;/i&gt; locus, and &lt;i&gt;H-Ras&lt;/i&gt;, respectively. Furthermore, a transcriptional program that defines the cellular response to p53 inactivation was an excellent predictor of metastasis development and bad prognosis in breast cancer patients. Deciphering these transformation fingerprints, which are affected by the most common oncogenic mutations, provides considerable insight into regulatory circuits controlling malignant transformation and will hopefully open new avenues for rational therapeutic decisions.&lt;/p&gt;&lt;/div&gt;
Thermally Activated Bright-State Delayed Blue Photoluminescence from InP Quantum Dots (2022)

Thermally activated delayed photoluminescence (TADPL) generated from organic chromophore-functionalized quantum dots (QDs) is potentially beneficial for persistent light generation, QD-based PL sensors, and photochemical synthesis. While previous research demonstrated that naphthoic acid-functionalized InP QDs can be employed as low-toxicity, blue-emissive TADPL materials, the electron trap states inherent in these nanocrystals inhibited the observation of TADPL emerging from the higher-lying bright states. Here, we address this challenge by employing the heterocyclic aromatic compound 8-quinolinecarboxylic acid (QCA), whose triplet energy is strategically positioned to bypass the electron trap states in InP QDs. Transient absorption and photoluminescence spectroscopies revealed the generation of bright-state TADPL from QCA-functionalized InP QDs resulting from a nearly quantitative Dexter-like triplet-triplet energy transfer (TTET) from photoexcited InP QDs to surface-anchored QCA chromophores followed by reverse TTET from these bound molecules to the InP QDs. This modification resulted in a 119-fold increase in the average PL intensity decay time with respect to the as-synthesized InP QDs.
ChemInform Abstract: A Facile Synthesis of N‐Aryl‐N‐hydroxyformamides from N‐Arylhydroxylamines. (1990)

Abstract Acetic formic anhydride (III) is prepared as shown and immediately used in the formylation reaction of the hydroxylamines (IV).
Invited Review Article: “Hands-on” laser-driven ion acceleration: A primer for laser-driven source development and potential applications (2016)

An overview of progress and typical yields from intense laser-plasma acceleration of ions is presented. The evolution of laser-driven ion acceleration at relativistic intensities ushers prospects for improved functionality and diverse applications which can represent a varied assortment of ion beam requirements. This mandates the development of the integrated laser-driven ion accelerator system, the multiple components of which are described. Relevant high field laser-plasma science and design of controlled optimum pulsed laser irradiation on target are dominant single shot (pulse) considerations with aspects that are appropriate to the emerging petawatt era. The pulse energy scaling of maximum ion energies and typical differential spectra obtained over the past two decades provide guidance for continued advancement of laser-driven energetic ion sources and their meaningful applications.
Characterization of Four Novel dsRNA Viruses Isolated from Mucor hiemalis Strains (2021)

We previously screened the total nucleic acid extracts of 123 <i>Mucor</i> strains for the presence of dsRNA molecules without further molecular analyses. Here, we characterized five novel dsRNA genomes isolated from four different <i>Mucor</i>&nbsp;<i>hiemalis</i> strains with next-generation sequencing (NGS), namely Mucor hiemalis virus 1a (MhV1a) from WRL CN(M) 122; Mucor hiemalis virus 1b (MhV1b) from NRRL 3624; Mucor hiemalis virus 2 (MhV2) from NRRL 3616; and Mucor hiemalis virus 3 (MhV3) and Mucor hiemalis virus (MhV4) from NRRL 3617 strains. Genomes contain two open reading frames (ORF), which encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In MhV1a and MhV1b, it is predicted to be translated as a fusion protein via -1 ribosomal frameshift, while in MhV4 via a rare +1 (or-2) ribosomal frameshift. In MhV2 and MhV3, the presence of specific UA<b>A</b><b>UG</b> pentanucleotide motif points to the fact for coupled translation termination and reinitialization. MhV1a, MhV2, and MhV3 are part of the clade representing the genus <i>Victorivirus</i>, while MhV4 is seated in <i>Totivirus</i> genus clade. The detected VLPs in <i>Mucor</i> strains were from 33 to 36 nm in diameter. Hybridization analysis revealed that the dsRNA molecules of MhV1a-MhV4 hybridized to the corresponding molecules.
Geburtshilfliche Pathologie im Schnittpunkt des traditionellen und modernen geburtshilflichen Systems in Korea (1983)

Die Mutterschaft, hier als die Gesamtheit der Beziehung der MutterKind-Dyade und der Abläufe um sie in Schwangerschaft, Geburt, Wochenbett und Laktation definiert, ist mit Gesundheitsrisiken für Mutter und Kind verbunden. Diese Risiken sind zwar dergestalt, daß sie im Verlauf der Menschheitsgeschichte das Überleben der Spezies Homo sapiens nicht beeinträchtigt haben, sie sind aber eine erhebliche Belastung für das betroffene Individuum und seine Umgebung. Verschiedene Kulturen verarbeiten diese Belastung auf unterschiedliche Weise. Während in vielen traditionellen Kulturen diese Risiken, z.B. etwa ein totes Kind, starke Blutungen, Geburtskanalverletzungen, Fieber etc., von den Beteiligten noch als ‘normale’ Begleiterscheinung der Mutterschaft klaglos in Kauf genommen werden, hat sich in westlichen Gesellschaften die moderne Geburtshilfe als ein Fachgebiet innerhalb der modernen Medizin entwickelt, das diese Risiken bekämpft. Sie ist inzwischen ein hochspezialisiertes und technologisiertes, medizinisches Spezialgebiet, das physische Komplikationen der Mutterschaft weitgehend verhüten oder erfolgreich behandeln kann. In vielen traditionellen Gesellschaften werden diese Risiken nicht mit Aufmerksamkeit bedacht, und die Mutterschaft hat keine medizinische Bedeutung, sondern sie ist in erster Linie eine Funktion in der Strukturierung des Lebenszyklus der Frau, der Familie und des Gemeinwesens. Die Rolle der Gebärenden wird nicht mit Krankenrolle und Patientendasein definiert wie in der modernen Geburtshilfe.
Personalized Search based on Community through Automatic Analysis of Query Patterns (2009)

Since the existing Web search engines don't sufficiently reflect user's search intent, it is very difficult to find out accurate information that users want to find. Therefore, a lot of researches, study for personalized search, to enhance satisfaction of Web search results by analyzing search pattern and applying it to search are in progress in these days. Web searchers can more efficiently find information and easily obtain appropriate information through the personalized search. In this paper, we propose the personalized search based on community through the analysis of web users' query patterns and interest. Consequently, when applying query frequency, interest and community to web search, we are able to the confirm that the search results which hit to the search intent of the individual are provided.