gebhart/patrepeval huggingface dataset:
Silicification: The Processes by Which Organisms Capture and Mineralize Silica (2003)

Research Article| January 03, 2003 Silicification: The Processes by Which Organisms Capture and Mineralize Silica Carole C. Perry Carole C. Perry Division of Chemistry, Interdisciplinary Biomedical Research Centre, The Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, United Kingdom Search for other works by this author on: GSW Google Scholar Author and Article Information Carole C. Perry Division of Chemistry, Interdisciplinary Biomedical Research Centre, The Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, United Kingdom Publisher: Mineralogical Society of America First Online: 03 Mar 2017 © The Mineralogical Society Of America Reviews in Mineralogy and Geochemistry (2003) 54 (1): 291–327. https://doi.org/10.2113/0540291 Article history First Online: 03 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Carole C. Perry; Silicification: The Processes by Which Organisms Capture and Mineralize Silica. Reviews in Mineralogy and Geochemistry 2003;; 54 (1): 291–327. doi: https://doi.org/10.2113/0540291 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyReviews in Mineralogy and Geochemistry Search Advanced Search Silicification is widespread in the biological world and occurs in bacteria, single-celled protists, plants, invertebrates and vertebrates. Minerals formed in the biological environment often show unusual physical properties (e.g., strength, degree of hydration) and often have structures that exhibit order on many length scales. The minerals are formed from an environment that is undersaturated with respect to silicon and under conditions of around neutral pH and low temperature ca. 4–40°C. Formation of the mineral may occur intra- or extra-cellularly and specific biochemical locations for mineral deposition that include lipids, proteins and carbohydrates are known. The significance of the cellular machinery... You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Recommendations for appropriate statistical practice in toxicologic experiments. (1984)

Appropriate statistical practice in toxicologic research is reviewed. The problem centers on the antagonistic needs to discover toxic effects and avoid false indictments of harmless compounds. Specific problems which distort error rates include having many dependent variables, conducting many tests on a variable, data snooping, lack of statistical power and 5) violations of statistical assumptions. Solution strategies include top down planning, designing efficient experiments, balancing type I and type II error rates, selecting hypotheses and 5) using appropriate statistical analysis methods. Top down planning and the "leapfrog" design strategy are particularly emphasized.
Linkage at 5q14.3–15 in multiplex systemic lupus erythematosus pedigrees stratified by autoimmune thyroid disease (2005)

Abstract Objective To identify genetic effects potentially shared between systemic lupus erythematosus (SLE) and autoimmune thyroiditis (AITD). Methods Families from the Lupus Multiplex Registry and Repository were studied in which there was at least 1 member who had both SLE and AITD (Graves' disease or Hashimoto thyroiditis). Genome scan genotyping findings in these pedigrees were evaluated for evidence of genetic linkage, by the maximum‐likelihood parametric method. Nineteen pedigrees were used in the initial genome scan. Subsequently, an independent sample of 16 pedigrees was used to replicate findings. Results Studies of the first set of 19 pedigrees yielded a 2‐point parametric logarithm of odds (LOD) of 4.97, which was independently confirmed in the replication sample of 16 pedigrees (LOD 2.89). For all 35 pedigrees together, the 2‐point LOD was 7.86, under a dominant model used for screening with 90% penetrance and a disease allele frequency of 10%. The multipoint locus homogeneity LOD in the 35 pedigrees was 6.90 (α = 1.0) at 5q14.3–15 between D5S1725 and D5S1453, a 12‐cM interval, with the peak at D5S1462 at 96.64 cM (nonparametric linkage P = 0.00002). Fine mapping further confirmed the genetic linkage effect and narrowed the region likely to contain the gene to ∼5 Mb. Conclusion These results suggest that stratifying SLE pedigrees by the presence of other autoimmune disorders may facilitate the discovery of genes related to SLE and that 5q14.3–15 harbors a susceptibility gene shared by SLE and AITD.
Changes in gut viral and bacterial species correlate with altered 1,2-diacylglyceride levels and structure in the prefrontal cortex in a depression-like non-human primate model (2022)

Major depressive disorder (MDD) is a debilitating mental disease, but its underlying molecular mechanisms remain obscure. Our previously established model of naturally occurring depression-like (DL) behaviors in Macaca fascicularis, which is characterized by microbiota-gut-brain (MGB) axis disturbances, can be used to interrogate how a disturbed gut ecosystem may impact the molecular pathology of MDD. Here, gut metagenomics were used to characterize how gut virus and bacterial species, and associated metabolites, change in depression-like monkey model. We identified a panel of 33 gut virus and 14 bacterial species that could discriminate the depression-like from control macaques. In addition, using lipidomic analyses of central and peripheral samples obtained from these animals, we found that the DL macaque were characterized by alterations in the relative abundance, carbon-chain length, and unsaturation degree of 1,2-diacylglyceride (DG) in the prefrontal cortex (PFC), in a brain region-specific manner. In addition, lipid-reaction analysis identified more active and inactive lipid pathways in PFC than in amygdala or hippocampus, with DG being a key nodal player in these lipid pathways. Significantly, co-occurrence network analysis showed that the DG levels may be relevant to the onset of negative emotions behaviors in PFC. Together our findings suggest that altered DG levels and structure in the PFC are hallmarks of the DL macaque, thus providing a new framework for understanding the gut microbiome's role in depression.
The exact solution of self-consistent equations in the scanning near-field optic microscopy problem (1999)

The macroscopic approach that allows one to obtain an exact solution of the self-consistent equation of the Lippmann-Schwinger type is developed. The main idea of our method consist in usage of diagram technique for exact summation of the infinite series corresponding to the iteration procedure for solving the self-consistent integral equation. The method developed is applied to calculations of near-field optical images obtained in illumination mode. It is assumed that the system under consideration consists of an object illuminated by the field scattered by a small probe. This assumption allows us to consider multiple scattering between a (point-like) probe and an extended object as well as inside the object. The exact solution for the self-consistent field is then obtained in terms of effective susceptibility of the probe-object system. Application of our method to the description of orientation of molecular complexes at the surface is discussed.
Insights into Asparaginase from Endophytic Fungus Lasiodiplodia theobromae: Purification, Characterization and Antileukemic Activity (2022)

Endobiotic fungi are considered as a reservoir of numerous active metabolites. Asparaginase is used as an antileukemic drug specially to treat acute lymphoblastic leukaemia. The presented study aims to optimize the media conditions, purify, characterize, and test the antileukemic activity of the asparaginase induced from <i>Lasiodiplodia theobromae</i>. The culture medium was optimized using an experiment designed by The Taguchi model with an activity ranging from 10 to 175 IU/mL. Asparaginase was induced with an activity of 315 IU/mL. Asparaginase was purified with a specific activity of 468.03 U/mg and total activity of 84.4 IU/mL. The purified asparaginase showed an approximate size of 70 kDa. The purified asparaginase showed an optimum temperature of 37 °C and an optimum pH of 6. SDS reduced the activity of asparaginase to 0.65 U/mL while the used ionic surfactants enhanced the enzyme activity up to 151.92 IU/mL. The purified asparaginase showed a K<sub>m</sub> of 9.37 µM and V<sub>max</sub> of 127.00 µM/mL/min. The purified asparaginase showed an IC<sub>50</sub> of 35.2 ± 0.7 IU/mL with leukemic M-NFS-60 cell lines and CC<sub>50</sub> of 79.4 ± 1.9 IU/mL with the normal WI-38 cell line. The presented study suggests the use of endophytic fungi as a sustainable source for metabolites such as asparaginase, provides an opportunity to develop a facile, eco-friendly, cost-effective, and rapid synthesis of antileukemic drugs, which have the potential to be used as alternative and reliable sources for potent anticancer agents.
α-Halogenation of triphenylene-based discotic liquid crystals: towards a chiral nucleus (1997)

In an attempt to prepare chiral discotic liquid crystals based on a helically twisted triphenylene nucleus a route has been developed for the introduction of α-fluoro, -chloro and -bromo substituents and it is shown that multiple α-halogenation is also possible. The monosubstituted derivatives all show enhanced mesophase stability whilst formation of the mesophase is suppressed for the polyhalogenated derivatives. Rather surprisingly, reaction of 2,3,6,7,10,11-hexahexyloxytriphenylene (HAT6) with iodine monochloride results in chlorination rather than iodination.
Devising an effective fundraising strategy (2017)

A carefully thought-out fundraising strategy that links closely with your school improvement plan could be considered an essential for schools. Expert Brin Best discusses how to devise an effective fundraising strategy for your school
An architecture for co-ordinated monitoring for multi-provider cloud platforms (2014)

In recent years there has been a considerable research surrounding multi-provider cloud platforms. Various architectures for realizing such systems have been proposed. However, most of this research has overlooked (or mentioned in passing) a vital aspect for the multi-provider deployment of platforms: the design of a monitoring systems to co-ordinate the monitoring systems in those platforms. This paper presents an architecture for a centralized monitoring system that coordinates the operation of individual domain-dependent monitoring systems. Our architecture enables the possibility for a global administrator to centrally define resource specific monitoring policies which can then be cascaded to the respective monitoring sub-systems. Owners of those sub-systems can also define their own policies based on the cascaded policies and their own requirements and preferences. We demonstrate with an example how this can be achieved within our innovative architecture.
A Motorcycle Multi-Body Model for Real Time Simulations Based on the Natural Coordinates Approach (2002)

This paper presents an eleven degrees of freedom, non-linear, multi-body dynamics model of a motorcycle. Front and rear chassis, steering system, suspensions and tires are the main features of the model. An original tire model was developed, which takes into account the geometric shape of tires and the elastic deformation of tire carcasses. This model also describes the dynamic behavior of tires in a way similar to relaxation models. Equations of motion stem from the natural coordinates approach. First, each rigid body is described with a set of fully cartesian coordinates. Then, links between the bodies are obtained by means of algebraic equations. This makes it possible to obtain simple equations of motion, even though the coordinates are redundant. The model was implemented in a Fortran code, named FastBike. In order to test the code, both simulated and real slalom and lane change maneuvers were carried out. A very good agreement between the numerical simulations and experimental test was found. The comparison of FastBike's performance with those of some commercial software shows that first is much faster than others. In particular, real time simulations can be carried out using FastBike and it can be employed on a motorcycle simulator.
Time-Step Volume-Preserving Control of Chemical Reactors (2007)

We present a general control and optimization strategy based on time-step state space volume control. This is performed by maintaining the divergence of the system close to zero. The on-line implementation is shown for batch chemical reactors and the simulated results are compared with a traditional control scheme.
Multi-level Knowledge Distillation via Knowledge Alignment and Correlation (2020)

Knowledge distillation (KD) has become an important technique for model compression and knowledge transfer. In this work, we first perform a comprehensive analysis of the knowledge transferred by different KD methods. We demonstrate that traditional KD methods, which minimize the KL divergence of softmax outputs between networks, are related to the knowledge alignment of an individual sample only. Meanwhile, recent contrastive learning-based KD methods mainly transfer relational knowledge between different samples, namely, knowledge correlation. While it is important to transfer the full knowledge from teacher to student, we introduce the Multi-level Knowledge Distillation (MLKD) by effectively considering both knowledge alignment and correlation. MLKD is task-agnostic and model-agnostic, and can easily transfer knowledge from supervised or self-supervised pretrained teachers. We show that MLKD can improve the reliability and transferability of learned representations. Experiments demonstrate that MLKD outperforms other state-of-the-art methods on a large number of experimental settings including different (a) pretraining strategies (b) network architectures (c) datasets (d) tasks.
Multiple nonlinear prediction of S&P500 returns using an ANFIS (2015)

Diese Arbeit präsentiert mit dem ANFIS ein Konzept aus dem Machine Learning mit dessen Hilfe die Rendite des S&amp;P500 nichtlinear vorhergesagt wird. In Anlehnung an Welch and Goyal (2008) wird als Vergleichsgröße zur Renditevorhersage der historische Durchschnitt der Rendite verwendet. Das ANFIS wird auf Daten angewendet, welche über 1-jährige Zeiträume und 2-jährige Zeiträume erhoben wurden. Bei der Verwendung der Daten der 1-jährigen Zeiträume gelingt es mit dem ANFIS nicht den historischen Durchschnitt der Rendite als Vergleichsgröße zu schlagen. Angewendet auf die Daten der 2-jährigen Zeiträume ist es jedoch möglich die Vergleichsgröße zu schlagen.
Quantum randomness extraction for various levels of characterization of the devices (2014)

11pages, 3 figures. Section II is a concise review of works on randomness, structured around three classes of adversarial power and three levels of characterization of the devices. In Section V, we discuss some subtleties of randomness extraction when an ancilla is required (POVMs, pointer measurements)
Parallel Parameter Tuning for Applications with Performance Variability (2005)

In this paper, we present parallel on-line optimization algorithms for parameter tuning of parallel programs. We employ direct search algorithms that update parameters based on real-time performance measurements. We discuss the impact of performance variability on the accuracy and efficiency of the optimization algorithms and proposed modified versions of the direct search algorithms to cope with it. The modified version uses multiple samples instead of single sample to estimate the performance more accurately. We present preliminary results that the performance variability of applications on clusters is heavy tailed. Finally, we studay and demonstrate the performance of the proposed algorithms for real scientific application.
Numerical Derivation of Necessary Conditions for Indirect Trajectory Optimization (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-3939.vid Current indirect optimal control problem (IOCP) solvers, like beluga or PINs, use symbolic math to derive the necessary conditions to solve the IOCP. The purpose of this paper is to present a framework that extends those solvers to derive the necessary conditions of an IOCP with fully numeric methods. This aim was achieved by implementing both symbolic math and algorithmic differentiation (AD) as methods to derive the IOCP necessary conditions into a new solver called Giuseppe. The solution to the Goddard Rocket problem and a space shuttle descent problem are solved using both symbolic math and AD in Giuseppe and compared in this paper. The AD method yields the exact same precision as the symbolic methods, but takes significantly less time than the non-JIT-compiled symbolic method. Additionally, using AD will allow solutions to problems with lookup tables that cannot be formulated and solved using symbolic math.
The function of BCL9 in Wnt/β-catenin signaling and colorectal cancer cells (2008)

BCL9 is required for efficient beta-catenin-mediated transcription in human cell lines whose Wnt pathway is active, including colorectal cancer cells, indicating its potential as a drug target in colorectal cancer.
Transrectal ultrasound image processing for brachytherapy applications (2006)

In this thesis, we propose a novel algorithm for detecting needles and their corresponding implanted radioactive seed locations in the prostate. The seed localization process is carried out efficiently using separable Gaussian filters in a probabilistic Gibbs random field framework. An approximation of the needle path through the prostate volume is obtained using a polynomial fit. The seeds are then detected and assigned to their corresponding needles by calculating local maxima of the voronoi region around the needle position. In our experiments, we were able to successfully localize over 85% of the implanted seeds. Furthermore, as a regular part of a brachytherapy cancer treatment, patient’s prostate is scanned using a trans-rectal ultrasound probe, its boundary is manually outlined, and its volume is estimated for dosimetry purposes. In this thesis, we also propose a novel semi-automatic segmentation algorithm for prostate boundary detection that requires a reduced amount of radiologist’s input, and thus speeds up the surgical procedure. Saved time can be used to re-scan the prostate during the operation and accordingly adjust the treatment plan. The proposed segmentation algorithm utilizes texture differences between ultrasound images of the prostate tissue and the surrounding tissues. It is carried out in 5 the polar coordinate system and it uses three-dimensional data correlation to improve the smoothness and reliability of the segmentation. Test results show that the boundary segmentation obtained from the algorithm can reduce manual input by the factor of 3, without significantly affecting the accuracy of the segmentation (i.e. semi-automatically estimated prostate volume is within 90% of the original estimate).
Correct Assembly of Iron-Sulfur Cluster FS0 into Escherichia coli Dimethyl Sulfoxide Reductase (DmsABC) Is a Prerequisite for Molybdenum Cofactor Insertion (2011)

The FS0 [4Fe-4S] cluster of the catalytic subunit (DmsA) of Escherichia coli dimethyl sulfoxide reductase (DmsABC) plays a key role in the electron transfer relay. We have now established an additional role for the cluster in directing molybdenum cofactor assembly during enzyme maturation. EPR spectroscopy indicates that FS0 has a high spin ground state (S = 3/2) in its reduced form, resulting in an EPR spectrum with a peak at g ∼ 5.0. The cluster is predicted to be in close proximity to the molybdo-bis(pyranopterin guanine dinucleotide) (Mo-bisPGD) cofactor, which provides the site of dimethyl sulfoxide reduction. Comparison with nitrate reductase A (NarGHI) indicates that a sequence of residues ((18)CTVNC(22)) plays a role in both FS0 and Mo-bisPGD coordination. A DmsA(ΔN21) mutant prevented Mo-bisPGD binding and resulted in a degenerate [3Fe-4S] cluster form of FS0 being assembled. DmsA belongs to the Type II subclass of Mo-bisPGD-containing catalytic subunits that is distinguished from the Type I subclass by having three rather than two residues between the first two Cys residues coordinating FS0 and a conserved Arg residue rather than a Lys residue following the fourth cluster coordinating Cys. We introduced a Type I Cys group into DmsA in two stages. We changed its sequence from (18)C(A)TVNC(B)GSRC(C)P(27) to (18)C(A)TYC(B)GVGC(C)G(26) (similar to that of formate dehydrogenase (FdnG)) and demonstrated that this eliminated both Mo-bisPGD binding and EPR-detectable FS0. We then combined this change with a DmsA(R61K) mutation and demonstrated that this additional change partially rescued Mo-bisPGD insertion.
QLIF-32. MEETING THE PATIENTS - MEETING THE NEEDS: PLATFORMS FOR PATIENTS USING OPTUNE® TO EXCHANGE EXPERTISE (2017)

Glioblastoma multiforme (GBM) patients and their relatives (PaR) face tremendous distress and psychological burden due to limited survival and neurological/neuropsychological deficits. Tumor Treating Fields (Optune®, TTFields 200 KHz) are a novel therapy for patients with newly diagnosed and recurrent GBM. TTFields being a new therapy, provide means for PaR to actively contribute to therapy, but require concerted attention. Additionally, PaR may have to adapt to social exposure. Our clinical experience in Germany shows an urgent need for personal exchange; especially expressed by female patients. Establishing patient-driven support groups is limited mainly due to the rapid clinical course alongside with neurological/neuropsychological deficits. The aim of this study is to systematically evaluate PaR`s needs, to implement a platform for personal exchange, and to analyze PaR`s benefit. Questionnaires to evaluate PaR`s needs regarding meeting other PaR included: preferences for time, frequency, and maximal travel distance. In addition, type/frequency of the desired professional support was queried. Quality of life and emotional function were determined 2 weeks before and after implementing this program by the questionnaires PHQ-2 and GAD-2. We assessed 9 PaR using Optune® at our department. 7/9 PaR expressed a strong demand to interact frequently with other PaR using Optune®, especially during the first months after start of treatment. Therefore, we established a meeting in a stimulating surrounding, accompanied and supported by the treating physician and psychologist. Additionally, an internet platform will be established allowing PaR exchanging contact data, but with access only for PaR using Optune®. According to the assessed needs, this pilot project established a communication platform for GBM-PaR using Optune®. Furthermore, we have implemented this concept into our clinical routine. Every PaR will be offered access to the internet platform and we encourage other centers to consider a guided PaR meeting.