gebhart/patrepeval huggingface dataset:
Ising-Based Consensus Clustering on Specialized Hardware (2020)

The emergence of specialized optimization hardware such as CMOS annealers and adiabatic quantum computers carries the promise of solving hard combinatorial optimization problems more efficiently in hardware. Recent work has focused on formulating different combinatorial optimization problems as Ising models, the core mathematical abstraction used by a large number of these hardware platforms, and evaluating the performance of these models when solved on specialized hardware. An interesting area of application is data mining, where combinatorial optimization problems underlie many core tasks. In this work, we focus on consensus clustering (clustering aggregation), an important combinatorial problem that has received much attention over the last two decades. We present two Ising models for consensus clustering and evaluate them using the Fujitsu Digital Annealer, a quantum-inspired CMOS annealer. Our empirical evaluation shows that our approach outperforms existing techniques and is a promising direction for future research.
Nutrition and Wound Healing (2006)

The relationship between nutrition and wound healing--after injury or surgical intervention--has been recognized for centuries. There is no doubt that adequate carbohydrate, fat, and protein intake is required for healing to take place, but research in the laboratory has suggested that other specific nutritional interventions can have significant beneficial effects on wound healing. Successful translation into the clinical arena, however, has been rare. A review of normal metabolism as it relates to wound healing in normoglycemic and diabetic individuals is presented. This is followed by an assessment of the current literature and the data that support and refute the use of specialized nutritional support in postoperative and wounded patients. The experimental evidence for the use of arginine, glutamine, vitamins, and micronutrient supplementation is described. Most of the experimental evidence in the field supporting the use of specialized nutritional support has not been borne out by clinical investigation. A summary of the clinical implications of the data is presented, with the acknowledgment that each patient's plan of care must be individualized to optimize the relationship between nutrition and wound healing.
Method for obtaining gas concentration with a phase-based metrology system (1998)

A new technique is presented for obtaining gas concentration by measuring the slope of the anomalous dispersion at a resonance. We describe the equations that govern this process using a Lorentz model and show that the slope of the anomalous dispersion is directly related to the absorption coefficient. The slope is obtained from an interferometric setup and a frequency modulation spectroscopy technique. Experimental data are presented that illustrate this technique for two different sample cells containing water vapor.
Variability of relative blood volume during haemodialysis (2000)

RBV changes during haemodialysis showed a considerable intra- and inter-individual variability that could not be explained by differences in UV. No correlation was observed between UV or changes in RBV and either blood pressure or the incidence of hypotension. Heart rate, however, was significantly correlated with RBV. Moreover, IVC diameter was only poorly correlated with RBV, suggesting a redistribution of blood towards the central venous compartment. These data indicate that RBV monitoring is of limited use in the prevention of dialysis-related hypotension, and that the critical level of reduction in RBV at which hypotension occurs depends on cardiovascular defence mechanisms such as sympathetic drive.
Screening Kinase Phosphorylation Motifs Using Peptide Libraries (2007)

INTRODUCTIONThis protocol describes a method for oriented peptide library screening. This method, combined with bioinformatics-based searches of protein sequence databases, provides a strategy for identifying substrates of particular protein kinases, including low-abundance proteins. In oriented peptide library screening, a very large number of peptides are synthesized simultaneously by solid-phase peptide synthesis, with all of the peptides containing either a single fixed Ser, Thr, or Tyr residue at an "orienting" position within the peptide sequence. The orienting residue in the collection of peptides serves as the phospho-acceptor during an in vitro phosphorylation reaction with the protein kinase of interest and is flanked by a series of degenerate positions, which contain a mixture of all possible amino acids. Only those peptides that contain favorable amino acids surrounding the fixed Ser, Thr, or Tyr residues will be preferentially phosphorylated by the kinase of interest. This subset of phosphorylated peptides can then be separated from the bulk of nonphosphorylated peptides using immobilized metal affinity chromatography (IMAC). The recovered phosphopeptides are sequenced in bulk by Edman degradation. By comparing the amount of each amino acid at each position flanking the fixed Ser, Thr, or Tyr in the phosphorylated peptides with the amount of each amino acid in the starting peptide library mixture, the affinity of the kinase for each amino acid in each position in the sequence is revealed. The end result of this process is a matrix of selection values that describes, in quantitative terms, the relative importance of each amino acid at each position within the kinase substrate motif, as well as the optimal peptide substrate sequence for that kinase. The matrix of kinase selectivity values can be used to search protein sequence databases and identify potential substrate proteins that contain the closest matches to the optimal protein kinase phosphorylation motif. These putative substrates can then be examined in vitro and in vivo to determine whether they are, in fact, kinase substrates under physiological conditions.
Strategic Bidding in a Multiunit Auction: An Empirical Analysis of Bids to Supply Electricity in England and Wales (1998)

I consider bidding behavior in the daily electricity auction in England and Wales. Theoretical work on uniform-price multiunit procurement auctions suggests that bidders offering more than one unit have an incentive to increase their bids at high quantities. If a bid sets a high equilibrium price, it applies to all inframarginal units. I find evidence of strategic bid increases in the electricity auctions. First, plants that are likely to be used after other plants are already operating bid more. Second, the larger supplier submits higher bids for similar plants. Last, bids for a given plant are slightly higher on days when more of the capacity that is typically inframarginal to that plant is available.
The methyl-CpG binding protein MBD1 is required for PML-RARα function (2006)

PML-RARalpha induces a block of hematopoietic differentiation and acute promyelocytic leukemia. This block is based on its capacity to inactivate target genes by recruiting histone deacetylase (HDAC) and DNA methyltransferase activities. Here we report that MBD1, a member of a conserved family of proteins able to bind methylated DNA, cooperates with PML-RARalpha in transcriptional repression and cellular transformation. PML-RARalpha recruits MBD1 to its target promoter through an HDAC3-mediated mechanism. Binding of HDAC3 and MBD1 is not confined to the promoter region but instead is spread over the locus. Knock-down of HDAC3 expression by RNA interference in acute promyelocytic leukemia cells alleviates PML-RAR-induced promoter silencing. We further demonstrate that retroviral expression of dominant-negative mutants of MBD1 in hematopoietic precursors compromises the ability of PML-RARalpha to block their differentiation and thus restored cell differentiation. Our results demonstrate that PML-RARalpha functions by recruiting an HDAC3-MBD1 complex that contributes to the establishment and maintenance of the silenced chromatin state.
Extension of tabulated design parameters for rectangular columns exposed to fire taking into account second‐order effects and various fire models (2014)

Abstract Fire, as one of the most severe load conditions, has an important impact on concrete structures. Not only does a fire affect the material strength, it affects structural stiffness and stability as well. A concrete column, compared with other structural members, in most cases has to cope with both vertical forces and bending moments transferred by slabs and beams. Consequently, it is essential to find a reliable and practical way of establishing interaction curves for the overall structural behaviour of concrete columns subjected to fire. In this paper, a cross‐sectional calculation method based on the material models of Eurocode 2 is explained and adopted in order to calculate interaction curves for a typical rectangular column exposed to the ISO 834 standard fire. Subsequently, an iterative approach is introduced to develop interaction curves taking into account second‐order effects in the case of all the four faces of a column exposed to fire. The maximum permissible slenderness ratios for columns in different fire durations are obtained and compared with Eurocode 2 provisions. Finally, this method is used to calculate the maximum permissible slenderness ratios for columns exposed to hydrocarbon and natural fires.
MEASUREMENT OF HEAD IMPACTS IN COLLEGIATE FOOTBALL PLAYERS (2007)

Less than 0.35% of impacts exceeding theoretical injury thresholds resulted in concussion. More injury data are required before any theoretical thresholds for injury can be confirmed. Coaches and sports medicine professionals should recognize that head impacts sustained in helmets-only practices are as severe as games or scrimmages; there seem to be no "light" days for football players.
Educazione bilingue e multiculturale, istruzione bilingue, immersione totale : quattro nozioni da definire (1998)

Many names are used in the language of sudents' families, school brochures, local educational authorities, etc. (and even in specialistic literature) to refer to bilingual education (in the broadest sense). The A. claims the necessity to define the notions involved more clearly. The notions the paper suggests to identify as separate ones are bilingual education, multicultural education, bilingual instruction and full immersion. In order to define the theoretical framework two sets of variables are chosen. The first set integrates the anthropological model of human relations (I, I and You, I and the Community) and the pedagogical model of educational goals (Self-promotion, Socialization, Culturization); the second set comes from the political sciences, namely from the theory of language policy which distinguishes two types of plurilingual societies, the Melting pot and the Rice salad. Inserting the four notions often referred to as bilingual education into the matrix of the framework above shows that they are quite different processes and should be differentiated, both in curriculum design and in the language used by schools and educational authorities, and in specialistic literature
<i>GLK</i> gene pairs regulate chloroplast development in diverse plant species (2002)

Chloroplast biogenesis is a complex process that requires close co-ordination between two genomes. Many of the proteins that accumulate in the chloroplast are encoded by the nuclear genome, and the developmental transition from proplastid to chloroplast is regulated by nuclear genes. Here we show that a pair of Golden 2-like (GLK) genes regulates chloroplast development in Arabidopsis. The GLK proteins are members of the GARP superfamily of transcription factors, and phylogenetic analysis demonstrates that the maize, rice and Arabidopsis GLK gene pairs comprise a distinct group within the GARP superfamily. Further phylogenetic analysis suggests that the gene pairs arose through separate duplication events in the monocot and dicot lineages. As in rice, AtGLK1 and AtGLK2 are expressed in partially overlapping domains in photosynthetic tissue. Insertion mutants demonstrate that this expression pattern reflects a degree of functional redundancy as single mutants display normal phenotypes in most photosynthetic tissues. However, double mutants are pale green in all photosynthetic tissues and chloroplasts exhibit a reduction in granal thylakoids. Products of several genes involved in light harvesting also accumulate at reduced levels in double mutant chloroplasts. GLK genes therefore regulate chloroplast development in diverse plant species.
Role of Lipid II and Membrane Thickness in the Mechanism of Action of the Lantibiotic Bovicin HC5 (2011)

Lantibiotics are antimicrobial peptides produced by Gram-positive bacteria, nisin being the most well-known member. Nisin inhibits peptidoglycan synthesis and forms pores at sensitive membranes upon interaction with lipid II, the essential bacterial cell wall precursor. Bovicin HC5, a bacteriocin produced by Streptococcus bovis HC5, has the putative N-terminal lipid II binding motif, and we investigated the mode of action of bovicin HC5 using both living bacteria and model membranes, with special emphasis on the role of lipid II. Bovicin HC5 showed activity against Staphylococcus cohnii and Staphylococcus warneri, but bovicin HC5 hardly interfered with the membrane potential of S. cohnii. In model membranes, bovicin HC5 was not able to cause carboxyfluorescein release or proton influx from DOPC vesicles containing lipid II. Bovicin HC5 blocked lipid II-dependent pore formation activity of nisin, and a high-affinity interaction with lipid II was observed (apparent binding constant [K(a)] = 3.1 × 10(6) M(-1)), with a 1:1 stoichiometry. In DOPC vesicles containing lipid II, bovicin HC5 was able to assemble with lipid II into a prepore-like structure. Furthermore, we observed pore formation activity of bovicin HC5, which was stimulated by the presence of lipid II, in thin membranes. Moreover, bovicin HC5 induced the segregation of lipid II into domains in giant model membrane vesicles. In conclusion, bovicin HC5 has a primary mode of action similar to that of nisin, but some differences regarding the pore-forming capacity were demonstrated.
Evaluation of Robust Spatial Pyramid Pooling Based on Convolutional Neural Network for Traffic Sign Recognition System (2020)

Traffic sign recognition (TSR) is a noteworthy issue for real-world applications such as systems for autonomous driving as it has the main role in guiding the driver. This paper focuses on Taiwan’s prohibitory sign due to the lack of a database or research system for Taiwan’s traffic sign recognition. This paper investigates the state-of-the-art of various object detection systems (Yolo V3, Resnet 50, Densenet, and Tiny Yolo V3) combined with spatial pyramid pooling (SPP). We adopt the concept of SPP to improve the backbone network of Yolo V3, Resnet 50, Densenet, and Tiny Yolo V3 for building feature extraction. Furthermore, we use a spatial pyramid pooling to study multi-scale object features thoroughly. The observation and evaluation of certain models include vital metrics measurements, such as the mean average precision (mAP), workspace size, detection time, intersection over union (IoU), and the number of billion floating-point operations (BFLOPS). Our findings show that Yolo V3 SPP strikes the best total BFLOPS (65.69), and mAP (98.88%). Besides, the highest average accuracy is Yolo V3 SPP at 99%, followed by Densenet SPP at 87%, Resnet 50 SPP at 70%, and Tiny Yolo V3 SPP at 50%. Hence, SPP can improve the performance of all models in the experiment.
Development of the 21-Gene Assay and Its Application in Clinical Practice and Clinical Trials (2008)

Several multigene markers that predict relapse more accurately than classical clinicopathologic features have been developed. The 21-gene assay was developed specifically for patients with estrogen receptor (ER)-positive breast cancer, and has been shown to predict distant recurrence more accurately that classical clinicopathologic features in patients with ER-positive breast cancer and negative axillary nodes treated with adjuvant tamoxifen; validation studies in this population led to its approval as a diagnostic test. In a similar population, it also may be used to assess the benefit of adding chemotherapy to hormonal therapy. Other validation studies indicate that it also predicts the risk of distant and local recurrence in other populations with ER-positive disease, including node-negative patients receiving no adjuvant therapy and patients with positive axillary nodes treated with doxorubicin-containing chemotherapy. The Trial Assigning Individualized Options for Treatment (TAILORx) is multicenter trial that integrates the 21-gene assay into the clinical decision-making process and is designed to refine the utility of the assay in clinical practice and to provide a resource for evaluating additional molecular markers as they are developed in the future.
In-Situ Formation of Biodegradable Hydrogels by Stereocomplexation of PEG−(PLLA)<sub>8</sub> and PEG−(PDLA)<sub>8</sub> Star Block Copolymers (2006)

Eight-arm poly(ethylene glycol)-poly(L-lactide), PEG-(PLLA)(8), and poly(ethylene glycol)-poly(D-lactide), PEG-(PDLA)(8), star block copolymers were synthesized by ring-opening polymerization of either L-lactide or D-lactide at room temperature in the presence of a single-site ethylzinc complex and 8-arm PEG (M(n) = 21.8 x 10(3) or 43.5 x 10(3)) as a catalyst and initiator, respectively. High lactide conversions (>95%) and well-defined copolymers with PLLA or PDLA blocks of the desired molecular weights were obtained. Star block copolymers were water-soluble when the number of lactyl units per poly(lactide) (PLA) block did not exceed 14 and 17 for PEG21800-(PLA)(8) and PEG43500-(PLA)(8), respectively. PEG-(PLA)(8) stereocomplexed hydrogels were prepared by mixing aqueous solutions with equimolar amounts of PEG-(PLLA)(8) and PEG-(PDLA)(8) in a polymer concentration range of 5-25 w/v % for PEG21800-(PLA)(8) star block copolymers and of 6-8 w/v % for PEG43500-(PLA)(8) star block copolymers. The gelation is driven by stereocomplexation of the PLLA and PDLA blocks, as confirmed by wide-angle X-ray scattering experiments. The stereocomplexed hydrogels were stable in a range from 10 to 70 degrees C, depending on their aqueous concentration and the PLA block length. Stereocomplexed hydrogels at 10 w/v % polymer concentration showed larger hydrophilic and hydrophobic domains as compared to 10 w/v % single enantiomer solutions, as determined by cryo-TEM. Correspondingly, dynamic light scattering showed that 1 w/v % solutions containing both PEG-(PLLA)(8) and PEG-(PDLA)(8) have larger "micelles" as compared to 1 w/v % single enantiomer solutions. With increasing polymer concentration and PLLA and PDLA block length, the storage modulus of the stereocomplexed hydrogels increases and the gelation time decreases. Stereocomplexed hydrogels with high storage moduli (up to 14 kPa) could be obtained at 37 degrees C in PBS. These stereocomplexed hydrogels are promising for use in biomedical applications, including drug delivery and tissue engineering, because they are biodegradable and the in-situ formation allows for easy immobilization of drugs and cells.
Perspective: Sign epistasis and genetic constraint on evolutionary trajectories. (2005)

Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.
Immunotherapeutic organoids (2013)

Therapeutic monoclonal antibodies have revolutionized the treatment of cancer and other diseases. However, several limitations of antibody-based treatments, such as the cost of therapy and the achievement of sustained plasma levels, should be still addressed for their widespread use as therapeutics. The use of cell and gene transfer methods offers additional benefits by producing a continuous release of the antibody with syngenic glycosylation patterns, which makes the antibody potentially less immunogenic. In vivo secretion of therapeutic antibodies by viral vector delivery or ex vivo gene modified long-lived autologous or allogeneic human mesenchymal stem cells may advantageously replace repeated injection of clinical-grade antibodies. Gene-modified autologous mesenchymal stem cells can be delivered subcutaneously embedded in a non-immunogenic synthetic extracellular matrix-based scaffold that guarantees the survival of the cell inoculum. The scaffold would keep cells at the implantation site, with the therapeutic protein acting at distance (immunotherapeutic organoid), and could be retrieved once the therapeutic effect is fulfilled. In the present review we highlight the practical importance of living cell factories for in vivo secretion of recombinant antibodies.
All-Optical 2R Regeneration Using a Non-Linear Vertical Cavity Semiconductor Optical Amplifier (2003)

All-optical 2R logic regeneration is demonstrated using a vertical cavity semiconductor optical amplifier. The optical switching threshold is 1 μ.W, with 10 dB gain and >6:1 (8dB) extinction ratio. Performance limits are also discussed.
Transition State Theory and Reaction Dynamics – An Overview (2001)

Introduction Crossing the Transition State in Solution Acid–Base Proton-Transfer Reactions in Solution Wave-Packet Evolution for Proton-Transfer Reactions
A Comparative Study of Feather and Synthetic Badminton Shuttlecock Aerodynamics (2010)

Badminton is a high drag game. The aerodynamic properties of badminton shuttlecocks are complex. As a bluff body, the shuttlecock generates high aerodynamic drag and steep flight trajectory. Although a series of studies on aerodynamic behaviour of spherical and ellipsoidal balls have been reported in the open literature, scant information is available in the public domain about the aerodynamic behaviour of badminton shuttlecocks. The primary objective of this work was to evaluate aerodynamic properties of a series of shuttlecocks under a range of wind speeds. The non-dimensional drag coefficient was determined and compared. The natural feather shuttlecock displayed lower drag coefficient at low speeds and significantly higher drag at high speeds. On the other hand, the synthetic shuttlecock demonstrated the opposite trends.