Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmon-Induced Nanolocalized Reduction of Diazonium Salts

Surface grafting from diazonium solutions triggered by localized surface plasmon has been investigated. An organic layer that is 20–30 nm thick is easily grafted onto gold nanoparticles (AuNPs) by visible-light illumination in a few minutes without any reducing agent or molecular photocatalyst. Grafting depends on the wavelength and polarization of the incident light. As a consequence, the orientation of the growth of the layer deposited on the AuNPs can be controlled by polarized light. Grafting is also highly enhanced between adjacent AuNPs or at the corners of triangular AuNPs, that is, in plasmonic hot spots. These results clearly demonstrate plasmon enhancement and strongly suggest that the transfer of hot electrons from the excited plasmonic NPs to the diazonium is the main mechanism. They also confirm that localized surface plasmon resonance can induce nanolocalized electrochemical reactions, thus contributing to the field of “plasmonic electrochemistry”.
Can Active Learning Experience Be Transferred?

Active learning is an important machine learning problem in reducing the human labeling effort. Current active learning strategies are designed from human knowledge, and are applied on each dataset in an immutable manner. In other words, experience about the usefulness of strategies cannot be updated and transferred to improve active learning on other datasets. This paper initiates a pioneering study on whether active learning experience can be transferred. We first propose a novel active learning model that linearly aggregates existing strategies. The linear weights can then be used to represent the active learning experience. We equip the model with the popular linear upper-confidence-bound (LinUCB) algorithm for contextual bandit to update the weights. Finally, we extend our model to transfer the experience across datasets with the technique of biased regularization. Empirical studies demonstrate that the learned experience not only is competitive with existing strategies on most single datasets, but also can be transferred across datasets to improve the performance on future learning tasks.
Accorciamenti, Hypocoristics, and Foot Structure: Against the Ternary Foot in Italian

This paper challenges the ternary foot as a possible foot type in Italian. This is contrary to the foot inventories proposed by a number of authors including Marotta (1997), Bafile (1996), Thornton (1996), and Nespor (1993). Within an Optimality Theoretic framework, it is shown that Foot-Binarity must be an undominated constraint in the language in order to account for both the limited distribution of the dactyl and optional secondary stress after antepenultimate main stress (as reported by Camilli 1965, Malagoli 1968, Lepschy & Lepschy 1988, and Lepschy 1992). It is argued that the dactylic effect is a result of final syllable extrametricality as suggested in analyses by Den Os & Kager (1986), Sluyters (1990), Jacobs (1994), and D'Imperio & Rosenthall (1999). The second half of the paper refutes the most compelling evidence for the ternary foot, namely tri-syllabic hypocoristic forms (Thornton 1996). All Italian truncation is shown to be consistent with undominated Foot-Binarity. It is furthermore argued that Spanish hypocoristic formation (Lipski 1995 and Pineros 2000a, b) differs from its Italian counterpart in that in the former, Contiguity-BT is low-ranked while in the latter it is undominated.
Molecular clock fork phylogenies: closed form analytic maximum likelihood solutions.

Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM) are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only for the simplest model-three-taxa, two-state characters, under a molecular clock. Quoting Ziheng Yang, who initiated the analytic approach,"this seems to be the simplest case, but has many of the conceptual and statistical complexities involved in phylogenetic estimation. "In this work, we give general analytic solutions for a family of trees with four-taxa, two-state characters, under a molecular clock. The change from three to four taxa incurs a major increase in the complexity of the underlying algebraic system, and requires novel techniques and approaches. We start by presenting the general maximum likelihood problem on phylogenetic trees as a constrained optimization problem, and the resulting system of polynomial equations. In full generality, it is infeasible to solve this system, therefore specialized tools for the molecular clock case are developed. Four-taxa rooted trees have two topologies-the fork (two subtrees with two leaves each) and the comb (one subtree with three leaves, the other with a single leaf). We combine the ultrametric properties of molecular clock fork trees with the Hadamard conjugation to derive a number of topology dependent identities. Employing these identities, we substantially simplify the system of polynomial equations for the fork. We finally employ symbolic algebra software to obtain closed formanalytic solutions (expressed parametrically in the input data). In general, four-taxa trees can have multiple ML points. In contrast, we can now prove that each fork topology has a unique(local and global) ML point.
Chimaeric anti‐interleukin 6 monoclonal antibodies in the treatment of advanced multiple myeloma: a phase I dose‐escalating study

Interleukin 6 plays a key role in the pathogenesis of multiple myeloma (MM). Therefore we conducted a phase I dose‐escalating study with chimaeric monoclonal anti‐IL6 antibodies (cMab) in MM patients resistant to second‐line chemotherapy. The cMab (CLB IL6/8; Kd 6.25 × 10−12 M) was given in two cycles of 14 daily infusions, starting on day 1 and day 28, repectively, with a daily dose of 5 mg in patients 1–3, 10 mg in patients 4–6, 20 mg in patients 7–9 and 40 mg in patients 10–12 (total dose 140 mg, 280 mg, 560 mg and 1120 mg of anti‐IL6, respectively). 11/12 patients had elevated pretreatment IL6 levels.
Evaluation of maternal infusion therapy during pregnancy for fetal development

The aim of this project was to study the possible association between maternal infusion treatments during pregnancy and variables of fetal development as well as the occurrence of congenital abnormalities (CA) in a case-control design. The large population-based data set of the Hungarian Case‑Control Surveillance of Congenital Abnormalities (HCCSCA) was evaluated based on the medically recorded infusion treatment during pregnancy. Of 22,843 case pregnant women who had newborns or fetuses with congenital abnormalities, 112 (0.5%), while of 38,151 control pregnant women who had newborn infants without any defects, 262 (0.7%), had infusion treatment during pregnancy. Infusion treatment was more frequent in the control group than in the case group with congenital abnormalities (adjusted POR with 945 95% CI: 0.7, 0.6-0.9) and there was no higher rate of maternal infusion treatments in any congenital abnormality group. Mean gestational age was shorter and mean birth weight was smaller in control newborn infants without CA born to mothers with infusion treatment during pregnancy than in the babies of mothers without infusion treatment. The prevalence of mild intrauterine growth retardation was more frequent in the fetuses of pregnant women with hyperemesis gravidarum treated with infusion. The results of the study suggest that infusion treatment of pregnant women did not associate with a higher risk of congenital abnormalities. In addition, the intravenous infusion of drugs has some, but limited efficacy to prevent the adverse effects of hyperemesis gravidarum and threatened preterm delivery.
From lab-scale film preparation to up- scale spinning fibre manufacturing of multiwall carbon nanotube/poly ethylene terephthalate composites

Carbon nanotubes are among the stiffest and strongest fibres known and they are thus considered as ideal fillers for polymeric fibre reinforcement. Carbon nanotube polymer composites have consequently attracted huge academic and industrial interest with thousands of relevant research works being published every year. In current work, we present a quite integrated study of multiwall carbon nanotube (MWCNT)-reinforced poly ethylene terephthalate (PET) composites prepared at laboratory scale along with industrial melt-spun fibres. For an optimum dispersion of the nanomaterial in the polymer matrix, we proceeded to appropriate functionalization of multiwall carbon nanotubes. The morphology of the composites was inspected by scanning electron microscope and transmission electron microscope, while the physical properties, such as crystallinity and orientation, by differential scanning calorimetry, X-ray diffraction and Raman spectroscopy. The addition of well-dispersed carbon nanotubes acts as a nucleation agent increasing the crystallization of poly ethylene terephthalate matrix, however, decreasing the orientation of either films or fibres. Carbon nanotubes /poly ethylene terephthalate polymer composite films present an increment of Young’s modulus and tensile strength to detriment of failure strain; namely, stiffness is accompanied by a less ductile behaviour. With the addition of carbon nanotubes to poly ethylene terephthalate fibres, a decrease in shrinkage and only a slight improvement in dimensional stability was attained; this once more explains the slow growth of their commercial applications since the mechanical properties of these materials still remain a fraction of the expected theoretical values.
OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

Flow cytometry is used increasingly in clinical research for cancer, immunology and vaccines. Technological advances in cytometry instrumentation are increasing the size and dimensionality of data sets, posing a challenge for traditional data management and analysis. Automated analysis methods, despite a general consensus of their importance to the future of the field, have been slow to gain widespread adoption. Here we present OpenCyto, a new BioConductor infrastructure and data analysis framework designed to lower the barrier of entry to automated flow data analysis algorithms by addressing key areas that we believe have held back wider adoption of automated approaches. OpenCyto supports end-to-end data analysis that is robust and reproducible while generating results that are easy to interpret. We have improved the existing, widely used core BioConductor flow cytometry infrastructure by allowing analysis to scale in a memory efficient manner to the large flow data sets that arise in clinical trials, and integrating domain-specific knowledge as part of the pipeline through the hierarchical relationships among cell populations. Pipelines are defined through a text-based csv file, limiting the need to write data-specific code, and are data agnostic to simplify repetitive analysis for core facilities. We demonstrate how to analyze two large cytometry data sets: an intracellular cytokine staining (ICS) data set from a published HIV vaccine trial focused on detecting rare, antigen-specific T-cell populations, where we identify a new subset of CD8 T-cells with a vaccine-regimen specific response that could not be identified through manual analysis, and a CyTOF T-cell phenotyping data set where a large staining panel and many cell populations are a challenge for traditional analysis. The substantial improvements to the core BioConductor flow cytometry packages give OpenCyto the potential for wide adoption. It can rapidly leverage new developments in computational cytometry and facilitate reproducible analysis in a unified environment.
Technical and Strategic Human Resource Management Effectiveness as Determinants of Firm Performance

We evaluated the impact of human resource (HR) managers' capabilities on HR management effectiveness and the latter's impact on corporate financial performance. For 293 U.S. firms, effectiveness was associated with capabilities and attributes of HR staff. We also found relationships between HR management effectiveness and productivity, cash flow, and market value. Findings were consistent across market and accounting measures of performance and with corrections for biases.
Localization of Calcium-Accumulating Structures in Striated Muscle Fibers

When frog muscle fibers from which the sarcolemma had been dissected away were perfused with a calcium solution and then treated with oxalate, electron-opaque material, probably calcium oxalate, accumulated in the terminal sacs of the sarcoplasmic reticulum. These regions of calcium accumulation were identified with the intracellular calcium sink that controls the relaxation phase of the contraction-relaxation cycle; their proximity to tubules implicated in intracellular stimulus conduction suggests that they might also be regions from which calcium is released to trigger contraction.
Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria

BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD) framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.
Refactoring for Parameterizing Java Classes

Type safety and expressiveness of many existing Java libraries and their client applications would improve, if the libraries were upgraded to define generic classes. Efficient and accurate tools exist to assist client applications to use generic libraries, but so far the libraries themselves must be parameterized manually, which is a tedious, time-consuming, and error-prone task. We present a type- constraint-based algorithm for converting non-generic libraries to add type parameters. The algorithm handles the full Java language and preserves backward compatibility, thus making it safe for existing clients. Among other features, it is capable of inferring wildcard types and introducing type parameters for mutually-dependent classes. We have implemented the algorithm as a fully automatic refactoring in Eclipse. We evaluated our work in two ways. First, our tool parameterized code that was lacking type parameters. We contacted the developers of several of these applications, and in all cases they confirmed that the resulting parameterizations were correct and useful. Second, to better quantify its effectiveness, our tool parameterized classes from already-generic libraries, and we compared the results to those that were created by the libraries' authors. Our tool performed the refactoring accurately-in 87% of cases the results were as good as those created manually by a human expert, in 9% of cases the tool results were better, and in 4% of cases the tool results were worse.
Working memory and DLPFC inefficiency in schizophrenia: the FBIRN study.

BACKGROUND The Functional Imaging Biomedical Informatics Network is a consortium developing methods for multisite functional imaging studies. Both prefrontal hyper- or hypoactivity in chronic schizophrenia have been found in previous studies of working memory. METHODS In this functional magnetic resonance imaging (fMRI) study of working memory, 128 subjects with chronic schizophrenia and 128 age- and gender-matched controls were recruited from 10 universities around the United States. Subjects performed the Sternberg Item Recognition Paradigm1,2 with memory loads of 1, 3, or 5 items. A region of interest analysis examined the mean BOLD signal change in an atlas-based demarcation of the dorsolateral prefrontal cortex (DLPFC), in both groups, during both the encoding and retrieval phases of the experiment over the various memory loads. RESULTS Subjects with schizophrenia performed slightly but significantly worse than the healthy volunteers and showed a greater decrease in accuracy and increase in reaction time with increasing memory load. The mean BOLD signal in the DLPFC was significantly greater in the schizophrenic group than the healthy group, particularly in the intermediate load condition. A secondary analysis matched subjects for mean accuracy and found the same BOLD signal hyperresponse in schizophrenics. CONCLUSIONS The increase in BOLD signal change from minimal to moderate memory loads was greater in the schizophrenic subjects than in controls. This effect remained when age, gender, run, hemisphere, and performance were considered, consistent with inefficient DLPFC function during working memory. These findings from a large multisite sample support the concept not of hyper- or hypofrontality in schizophrenia, but rather DLPFC inefficiency that may be manifested in either direction depending on task demands. This redirects the focus of research from direction of difference to neural mechanisms of inefficiency.
Attention Reverses the Effect of Prediction in Silencing Sensory Signals

Predictive coding models of perception suggest that predicted sensory signals are attenuated (silencing of prediction error). These models, though influential, are challenged by the fact that prediction sometimes enhances, rather than reduces task-relevant sensory signals, as in the case of spatial cueing experiments. One possible explanation is that in these experiments, prediction (i.e. whether a stimulus is likely to be presented) is confounded with attention (i.e. whether a stimulus requires a behavioural response), which is known to boost rather than reduce sensory signal. However, recent theoretical work on predictive coding inspires an alternative hypothesis, and suggests that attention and prediction may operate synergistically to improve the precision of perceptual inference. This model posits that attention leads to heightened weighting of sensory evidence, thereby reversing the sensory silencing by prediction. We factorially manipulated attention and prediction in an fMRI study to test the validity of this model. Our results support a predictive coding model wherein attention reverses the sensory attenuation of predicted signals. This may explain the seemingly contradictory findings in the literature regarding the effects of prediction on neural responses.
A descriptor system approach to H∞ control of linear time-delay systems

The output-feedback H/sub /spl infin// control problem is solved for continuous-time, linear, retarded and neutral-type systems. A delay-dependent solution is obtained in terms of linear matrix inequalities (LMIs) by using a descriptor model transformation of the system and by applying P. Park's inequality (1999) for bounding cross-terms. A state-feedback solution is derived for systems with polytopic parameter uncertainties. An output-feedback controller is then found by solving two LMIs, one of which is associated with a descriptor time-delay "innovation filter". The cases of instantaneous and delayed measurements are considered. Numerical examples are given which illustrate the effectiveness of the new theory.
High molecular weight stress proteins: Identification, cloning and utilisation in cancer immunotherapy

Abstract Although the large stress/heat shock proteins (HSPs), i.e. Hsp110 and Grp170, were identified over 30 years ago, these abundant and highly conserved molecules have received much less attention compared to other conventional HSPs. Large stress proteins act as molecular chaperones with exceptional protein-holding capability and prevent the aggregation of proteins induced by thermal stress. The chaperoning properties of Hsp110 and Grp170 are integral to the ability of these molecules to modulate immune functions and are essential for developing large chaperone complex vaccines for cancer immunotherapy. The potent anti-tumour activity of the Hsp110/Grp170-tumour protein antigen complexes demonstrated in preclinical studies has led to a phase I clinical trial through the National Cancer Institute’s rapid access to intervention development (RAID) programme that is presently underway. Here we review aspects of the structure and function of these large stress proteins, their roles as molecular chaperones in the biology of cell stress, and prospects for their use in immune regulation and cancer immunotherapy. Lastly, we will discuss the recently revealed immunosuppressive activity of scavenger receptor A that binds to Hsp110 and Grp170, as well as the feasibility of targeting this receptor to promote T-cell activation and anti-tumour immunity induced by large HSP vaccines and other immunotherapies.
Overexpression of Bcl-2 is associated with apoptotic resistance to the G-quadruplex ligand 12459 but is not sufficient to confer resistance to long-term senescence

The triazine derivative 12459 is a potent G-quadruplex interacting agent that inhibits telomerase activity. This agent induces time- and dose-dependent telomere shortening, senescence-like growth arrest and apoptosis in the human A549 tumour cell line. We show here that 12459 induces a delayed apoptosis that activates the mitochondrial pathway. A549 cell lines selected for resistance to 12459 and previously characterized for an altered hTERT expression also showed Bcl-2 overexpression. Transfection of Bcl-2 into A549 cells induced a resistance to the short-term apoptotic effect triggered by 12459, suggesting that Bcl-2 is an important determinant for the activity of 12459. In sharp contrast, the Bcl-2 overexpression was not sufficient to confer resistance to the senescence-like growth arrest induced by prolonged treatment with 12459. We also show that 12459 provokes a rapid degradation of the telomeric G-overhang in conditions that paralleled the apoptosis induction. In contrast, the G-overhang degradation was not observed when apoptosis was induced by camptothecin. Bcl-2 overexpression did not modify the G-overhang degradation, suggesting that this event is an early process uncoupled from the final apoptotic pathway.