gebhart/patrepeval huggingface dataset:
Investigation on Metastable Solution of Cellulose Dissolved in NaOH/Urea Aqueous System at Low Temperature (2011)

Our previous work has demonstrated that the cellulose solution dissolved in 7 wt % NaOH/12 wt % urea aqueous system precooled to -12 °C was metastable. It is worth noting that light scattering investigation on the cellulose solution at metastable state is difficult. In the present paper, the solution properties and dynamic behaviors of cellulose dissolved in the NaOH/urea aqueous solution were investigated by means of dynamic light scattering (DLS), to confirm the influence factors of the DLS measurement. The DLS results revealed that, after the dispersion of cellulose in NaOH/urea at low temperature, the single cellulose inclusion complexes (ICs) coexisted with minor IC aggregates even in very dilute solution. With increasing cellulose concentration or system temperature or prolonging storage time, the IC aggregation increased, as a result of the occurrence of the imperfect urea shell and the reconstruction of the hydrogen bonds between cellulose chains. The cellulose solution was relatively stable at low concentration and low storage temperature and for short storage time. In this case, the single cellulose inclusion complexes were the predominant species, and coexisted with minor IC aggregates, which was better to be used to measure the cellulose solution with DLS.
Overcoming Challenges in Fixed Point Training of Deep Convolutional\n Networks (2016)

It is known that training deep neural networks, in particular, deep\nconvolutional networks, with aggressively reduced numerical precision is\nchallenging. The stochastic gradient descent algorithm becomes unstable in the\npresence of noisy gradient updates resulting from arithmetic with limited\nnumeric precision. One of the well-accepted solutions facilitating the training\nof low precision fixed point networks is stochastic rounding. However, to the\nbest of our knowledge, the source of the instability in training neural\nnetworks with noisy gradient updates has not been well investigated. This work\nis an attempt to draw a theoretical connection between low numerical precision\nand training algorithm stability. In doing so, we will also propose and verify\nthrough experiments methods that are able to improve the training performance\nof deep convolutional networks in fixed point.\n
Possible Participation of Calcium–Regulating Factors in Senile Dementia in Elderly Female Subjects (1990)

um-related factors were compared in 60 elderly female subjects, who were classified into three groups as nondementia group (n = 18), groups of senile dementia of Alzheimer type (SDAT, n = 22) and of vascular type (VTD, n = 20). The group of SDAT showed significant decrease in serum calcium, and increases in serum parathyroid hormone and urinary Ca, and tendency of decrease in serum 1,25-dihydroxyvitamin D, compared to those of the nondementia group. However, the group of VTD, without showing these features, showed a tendency towards decreased serum calcitonin. These results suggest that Ca and Ca-regulating hormones may play several important and different roles in senile dementia.
A cost-effective synthesis of enantiopure ovothiol A from L-histidine, its natural precursor (2014)

Ovothiol A is a naturally occurring 4-mercaptohistidine derivative, and one of the most potent thiol-containing antioxidants. The synthesis of ovothiol A was elaborated by introducing the thiol group onto protected 3-methyl-L-histidine via halogenation and Ullmann reaction. This enantiopure synthesis of ovothiol A, which uses L-histidine as starting material, requires only five steps, and compared to prior synthesis, is both cost and time effiecent.
Preserving Catalytic Activity and Enhancing Biochemical Stability of the Therapeutic Enzyme Asparaginase by Biocompatible Multilayered Polyelectrolyte Microcapsules (2013)

The present study focuses on the formation of microcapsules containing catalytically active L-asparaginase (L-ASNase), a protein drug of high value in antileukemic therapy. We make use of the layer-by-layer (LbL) technique to coat protein-loaded calcium carbonate (CaCO3) particles with two or three poly dextran/poly-L-arginine-based bilayers. To achieve high loading efficiency, the CaCO3 template was generated by coprecipitation with the enzyme. After assembly of the polymer shell, the CaCO3 core material was dissolved under mild conditions by dialysis against 20 mM EDTA. Biochemical stability of the encapsulated L-asparaginase was analyzed by treating the capsules with the proteases trypsin and thrombin, which are known to degrade and inactivate the enzyme during leukemia treatment, allowing us to test for resistance against proteolysis by physiologically relevant proteases through measurement of residual l-asparaginase activities. In addition, the thermal stability, the stability at the physiological temperature, and the long-term storage stability of the encapsulated enzyme were investigated. We show that encapsulation of l-asparaginase remarkably improves both proteolytic resistance and thermal inactivation at 37 °C, which could considerably prolong the enzyme's in vivo half-life during application in acute lymphoblastic leukemia (ALL). Importantly, the use of low EDTA concentrations for the dissolution of CaCO3 by dialysis could be a general approach in cases where the activity of sensitive biomacromolecules is inhibited, or even irreversibly damaged, when standard protocols for fabrication of such LbL microcapsules are used. Encapsulated and free enzyme showed similar efficacies in driving leukemic cells to apoptosis.
Electrochemically induced actuation of liquid metal marbles (2013)

Controlled actuation of soft objects with functional surfaces in aqueous environments presents opportunities for liquid phase electronics, novel assembled super-structures and unusual mechanical properties. We show the extraordinary electrochemically induced actuation of liquid metal droplets coated with nanoparticles, so-called "liquid metal marbles". We demonstrate that nanoparticle coatings of these marbles offer an extra dimension for affecting the bipolar electrochemically induced actuation. The nanoparticles can readily migrate along the surface of liquid metals, upon the application of electric fields, altering the capacitive behaviour and surface tension in a highly asymmetric fashion. Surprising actuation behaviours are observed illustrating that nanoparticle coatings can have a strong effect on the movement of these marbles. This significant novel phenomenon, combined with unique properties of liquid metal marbles, represents an exciting platform for enabling diverse applications that cannot be achieved using rigid metal beads.
Adhesive Films from Dopamine‐Functionalized Polydimethylsiloxane Polymer Conetworks (2023)

Front Cover: In article 2200456 by Clément Mugemana and co-workers, adhesive films prepared from polydopamine-functionalized polydimethylsiloxane polymer co-networks with tunable stiffness and nanoscale phase-separated morphologies are presented.
Theory of phase segregation in DNA assemblies containing two different base-pair sequence types (2016)

Spontaneous pairing of homologous DNA sequences-a challenging subject in molecular biophysics, often referred to as 'homology recognition'-has been observed in vitro for several DNA systems. One of these experiments involved liquid crystalline quasi-columnar phases formed by a mixture of two kinds of double stranded DNA oligomer. Both oligomer types were of the same length and identical stoichiometric base-pair composition, but the base-pairs followed a different order. Phase segregation of the two DNA types was observed in the experiments, with the formation of boundaries between domains rich in molecules of one type (order) of base pair sequence. We formulate here a modified 'X-Y model' for phase segregation in such assemblies, obtain approximate solutions of the model, compare analytical results to Monte Carlo simulations, and rationalise past experimental observations. This study, furthermore, reveals the factors that affect the degree of segregation. Such information could be used in planning new versions of similar segregation experiments, needed for deepening our understanding of forces that might be involved, e.g., in gene-gene recognition.
Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing (2001)

Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The current study investigates the hypothesis that splicing of tissue-specific alternative exons is regulated in part by control sequences in adjacent introns and that such elements may be recognized via computational analysis of exons sharing a highly specific expression pattern. We have identified 25 brain-specific alternative cassette exons, compiled a dataset of genomic sequences encompassing these exons and their adjacent introns and used word contrast algorithms to analyze key features of these nucleotide sequences. By comparison to a control group of constitutive exons, brain-specific exons were often found to possess the following: divergent 5' splice sites; highly pyrimidine-rich upstream introns; a paucity of GGG motifs in the downstream intron; a highly statistically significant over-representation of the hexanucleotide UGCAUG in the proximal downstream intron. UGCAUG was also found at a high frequency downstream of a smaller group of muscle-specific exons. Intriguingly, UGCAUG has been identified previously in a few intron splicing enhancers. Our results indicate that this element plays a much wider role than previously appreciated in the regulated tissue-specific splicing of many alternative exons.
EXPERIMENTAL AND NUMERICAL INVESTIGATIONS OF MATRIX DIFFUSION IN A FRACTURED SANDSTONE BLOC (2000)

Exploited coal seams are used to deposit residues from thermal energy andwaste incineration plants at North Rhine Westphalia, Germany. Such an undergroundrepository requires the proof that dissolved contaminants may not reach the biosphere.Numerical models may be used as tool to predict the local and temporal migration ofpollutants. In order to investigate the migration of heavy metals in a porous sandstone bloccontaining a single fracture two tracer experiments were performed under preciselydefined hydraulic flow conditions. The tracer experiments were performed applyingpyranine, cadmium and lead as solutes and the hydrochemical conditions correspond to adepth of 1000 m below ground surface. For the numerical model the fracture wasconsidered as a two-dimensional parallel plate conduit and the rock matrix was treated asa three-dimensional porous medium. Together with rock properties determined inlaboratory the model yielded a good agreement between measured and simulatedbreakthrough curves by calibrating the fracture aperture and longitudinal dispersion.
Mammalian cell lines can be efficiently established in vitro upon expression of the SV40 large T antigen driven by a promoter sequence derived from the human vimentin gene (1991)

The aim of this study was to investigate a new method to enhance the efficiency to create mammalian cell lines. Cell immortalization was achieved by intranuclear microinjection of a recombinant DNA construct composed of a constitutive promoter controlling the genes encoding immortalizing proteins; the sequences coding for the large T and small t antigens were fused downstream of regulatory elements from the vimentin gene, the activation of which characterizes the vast majority of cells growing in vitro. Data show that the efficiency of the immortalizing procedures using the SV40 early genes could be enhanced by the control elements derived from the human vimentin (HuVim) 5' sequences that contained nucleotides -878 to +93 from the CAP site. This HuVim 830-T/t recombinant was used to create cell lines from numerous primary cultures of different origins: rabbit, porcine and human endothelial cells, rabbit and bovine epithelial cells. A set of large T-expressing cells was derived, and these cells retained characteristics of differential cells: binding of Ulex europaeus lectin and synthesis of Factor VIII for human endothelial cells; network of cytokeratin for bovine oviductal cells and rabbit mammary cells.
Reduction mechanisms for defect densities in GaN using one- or two-step epitaxial lateral overgrowth methods (2000)

A transmission electron microscopy study of the reduction mechanisms for defect densities in epitaxial lateral overgrown (ELO) GaN films is presented. In the standard one step ELO, the propagation of defects under the mask is blocked, whereas the defects in the window regions thread up to the surface. We propose an alternative two step ELO method. In a first step, dislocations close to the edge of the (0001) top facet bend at 90°, thereby producing a drastic reduction in the density of defects above the window. After the coalescence, induced by lateral growth in a second step, dislocations are mainly observed in the coalescence boundaries. The density of defects is decreased to 2×10−7 cm−2 over the entire surface and areas nearly 5 μm wide with 5×106 cm−2 dislocations between the center of the windows and the coalescence boundaries are obtained.
Temporal Specification and Deductive Verification of a Distributed Component Model and Its Environment (2009)

In this paper we investigate the formalisation of distributed and long-running stateful systems using our normative temporal specification framework. We analyse aspects of a component-oriented Grid system, and the benefits of having a logic-based tool to perform automated and safe dynamic reconfiguration of its components. We describe which parts of this Grid system are involved in the reconfiguration process and detail the translation procedure into a state-based formal specification. Subsequently, we apply deductive verification to test whether dynamic reconfiguration can be performed. Finally, we analyse the procedure required to update our model for reconfiguration and justify the validity and the advantages of our methodology.
Fusarium solaniDNase Is a Signal for Increasing Expression of Nonhost Disease Resistance Response Genes, Hypersensitivity, and Pisatin Production (1995)

The inoculation of pea endocarp tissue with the bean pathogen Fusarium solani f. sp. phaseoli results in a non-host resistance response causing a complete cessation of fungal growth within 6 to 8 h. In addition to previously reported elicitation by chitosan, we now report that components of this response are also induced by a DNase released from this fungus. A single band of protein corresponding with DNase activity elicits phytoalexin production and the accumulation of RnA homologous with the pathogenesis-related (PR) genes DRR49, DRR206, and DRR230. Both the enzyme activity and the eliciting potential of the Fusarium DNase (Fsp DNase) are heat stable but susceptible to digestion by proteinase K. Fsp DNase mimics the intact fungus in inducing resistance against F. solani f. sp. pisi. Also, Fsp DNase causes similar cytologically detectable changes in pea tissue, such as increasing hypersensitive discoloration and diminishing fluorescence of Hoechst 33342-stained nuclei and fluorescein diacetate stained cells.
Molecular mechanisms of neuroprotective action of immunosuppressants ‐ facts and hypotheses (2004)

Cyclosporin A (CsA) and FK506 (Tacrolimus) are short polypeptides which block the activation of lymphocytes and other immune system cells. Immunosuppressants exert neuroprotective and neurotrophic action in traumatic brain injury, sciatic nerve injury, focal and global ischemia in animals. Their neuroprotective actions are not understood and many hypotheses have been formed to explain such effects. We discuss a role of drug target--calcineurin in neuroprotective action of immunosuppressants. Protein dephosphorylation by calcineurin plays an important role in neuronal signal transduction due to its ability to regulate the activity of ion channels, glutamate release, and synaptic plasticity. In vitro FK506 protects cortex neurons from NMDA-induced death, augments NOS phosphorylation inhibiting its activity and NO synthesis. However, in vivo experiments demonstrated that FK506 in neuroprotective doses did not block excitotoxic cell death nor did it alter NO production during ischemia/reperfusion. Tissue damage in ischemia is the result of a complex pathophysiological cascade, which comprises a variety of distinct pathological events. Resident non-neuronal brain cells respond rapidly to neuronal cell death and may have both deleterious and useful role in neuronal damage. There is increasing evidence that reactive gliosis and post-ischemic inflammation involving microglia contribute to ischemic damage. We have demonstrated that FK506 modulates hypertrophic/proliferative responses and proinflammatory cytokine expression in astrocytes and microglia in vitro and in focal transient brain ischemia. Our findings suggest that astrocytes and microglia are direct targets of FK506 and modulation of glial response and inflammation is a possible mechanism of FK506-mediated neuroprotection in ischemia.
Marinesco-Sjögren Syndrome: Neuroradiologic Findings (1999)

We report the neuroradiologic manifestations of Marinesco-Sjögren Syndrome, an autosomal recessive disorder characterized by cerebellar ataxia, congenital cataracts, mental and physical retardation, skeletal anomalies and myopathy. Our patient population included eight patients (five males and three females), aged 4 to 56 years, with mental retardation, cerebellar ataxia and myopathy. Clinical and genetic evaluations were performed in all patients. Four patients underwent muscle biopsies. Nine CT examinations, seven MR examinations and two lateral skull films were performed. All patients had absent lenses and hypoplasia of vermis and cerebellar hemispheres. All except one (who had a posterior fossa arachnoid cyst) had a small posterior fossa. The neuroradiologic hallmarks of the disease are cerebellar hypoplasia, small posterior fossa and absence of the lens secondary to early cataract extraction. The role of imaging is to suggest this syndrome in the differential diagnosis of small posterior fossa or hypoplastic cerebellum and congenital cataracts. The presence of characteristic clinical findings and history of consanguineous marriage help in reaching the final diagnosis.
Parallel Automated Flow Synthesis of Covalent Protein Complexes That Can Inhibit MYC-Driven Transcription (2021)

Dysregulation of the transcription factor MYC is involved in many human cancers. The dimeric transcription factor complexes of MYC/MAX and MAX/MAX activate or inhibit, respectively, gene transcription upon binding to the same enhancer box DNA. Targeting these complexes in cancer is a long-standing challenge. Inspired by the inhibitory activity of the MAX/MAX dimer, we engineered covalently linked, synthetic homo- and heterodimeric protein complexes to attenuate oncogenic MYC-driven transcription. We prepared the covalent protein complexes (∼20 kDa, 167-231 residues) in a single shot via parallel automated flow synthesis in hours. The stabilized covalent dimers display DNA binding activity, are intrinsically cell-penetrant, and inhibit cancer cell proliferation in different cell lines. RNA sequencing and gene set enrichment analysis in A549 cancer cells confirmed that the synthetic dimers interfere with MYC-driven transcription. Our results demonstrate the potential of automated flow technology to rapidly deliver engineered synthetic protein complex mimetics that can serve as a starting point in developing inhibitors of MYC-driven cancer cell growth.
Interferometric measurement of dispersion in optical components (2002)

The development of high-quality tunable lasers and very bright, incoherent sources has made high-quality interferometric measurements available to the optical telecommunications industry. These measurements have advantages at the fundamental level because they allow linear-systems concepts and analysis to be applied to optical fiber systems. In particular, phase characteristics that have been previously measured as derivatives can be acquired directly, allowing more consistent evaluation and qualification of optical components for high-bit-rate systems.
Disruption of the Multiple Tumor Suppressor Gene MTS1/p16INK4a/CDKN2 by Illegitimate V(D)J Recombinase Activity in T-Cell Acute Lymphoblastic Leukemias (1997)

We have recently shown that the multiple tumor suppressor gene 1 (MTS1 ) encoding the p16(INK4a) and p19(ARF) cell-cycle inhibitors is inactivated by deletion or disruption in most human T-cell acute lymphoblastic leukemias (T-ALLs), representing the most frequent genetic event thus far described in this disease. To analyze the mechanism of these chromosomal events, we used cloning, sequencing, and/or polymerase chain reaction mapping to study 15 rearrangements occurring in the MTS1 locus. We found that these breakpoints occur in two clusters (MTS1(bcralpha) and MTS1(bcrbeta) ). The three rearrangements occurring in MTS1(bcralpha) correspond to a recurrent recombination juxtaposing 5' MTS2 exon 1 and 5' MTS1 exon 1alpha sequences. Breakpoints for 10 of 12 rearrangements within MTS1(bcrbeta) are located at a polymorphic (CA) repeat, suggesting that this sequence might play a role in the clustering. For both MTS1(bcralpha) and MTS1(bcrbeta), sequence analyses and PCR mapping experiments show that the tightly clustered breakpoints are located in the vicinity of heptamers whose sequence is similar to those involved in the V(D)J recombination. Moreover, short deletions, GC-rich random nucleotide additions, and clone-specific junctional sequences are present in all cases, further suggesting that the rearrangements are due to illegitimate V(D)J recombinase activity. These data are the first demonstration that a tumor suppressor gene can be inactivated by the V(D)J recombinational mechanism. Moreover, they reinforce the view that this process, normally required for T-cell differentiation, plays a crucial role in the pathogenesis of T-ALL.
<title>Efficient particle filters for joint tracking and classification</title> (2002)

Target tracking is usually performed using data from sensors such as radar, whilst the target identification task usually relies on information from sensors such as IFF, ESM or imagery. The differing nature of the data from these sensors has generally led to these two vital tasks being performed separately. However, it is clear that an experienced operator can observe behavior characteristics of targets and, in combination with knowledge and expectations of target type and likely activity, can more knowledgeably identify the target and robustly predict its track than any automatic process yet defined. Most trackers are designed to follow targets within a wide envelope of trajectories and are not designed to derive behavior characteristics or include them as part of their output. Thus, there is potential scope for both applying target type knowledge to improve the reliability of the tracking process, and to derive behavioral characteristics which may enhance knowledge about target identity and/or activity. In this paper we introduce a Bayesian framework for joint tracking and identification and give a robust and computationally efficient particle filter based algorithm for numerical implementation of the resulting recursions. Simulation results illustrating algorithm performance are presented.