Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Hemoglobin Associated with VEGF Inhibitors in Advanced Renal Cell Carcinoma

We retrospectively analyzed whether increased hemoglobin is a surrogate biomarker of efficacy for vascular endothelial growth factor (VEGF) inhibitors in advanced renal cell carcinoma (RCC) patients. Twelve patients were identified who had received bevacizumab alone or as combination therapy. Eleven patients experienced a rise in hemoglobin. Median change was 1.6 g/dL (0–4.0). Degree of peak increase correlated with longer progression-free survival (PFS) in metastatic patients: increase of < 15% yielded a 3.1-month median PFS compared to 8.2 months with rises > 15%. This study identifies increased hemoglobin as a possible consequence of VEGF inhibitors. The correlation with longer PFS suggests that rise in hemoglobin may be a surrogate biomarker of efficacy.
640 Gbit/s optical signal processing

Techniques for 640 Gbit/s generation, demultiplexing, clock recovery, add/drop multiplexing, wavelength conversion, transmission, channel identification and timing jitter tolerant switching is described. Various switching materials are explored, such as HNLF, SOA, chalcogenide, and PPLN.
The Induction of Seed Germination in Arabidopsis thaliana Is Regulated Principally by Phytochrome B and Secondarily by Phytochrome A

We examined whether spectrally active phytochrome A (PhyA) and phytochrome B (PhyB) play specific roles in the induction of seed germination in Arabidopsis thaliana (L.) Heynh. , using PhyA- and PhyB-null mutants, fre1-1 (A. Nagatani, J.W. Reed, J. Chory [1993] Plant Physiol 102: 269–277) and hy3-Bo64 (J. Reed, P.Nagpal, D.S. Poole, M. Furuya, J. Chory [1993] Plant Cell 5: 147–157). When dormant seeds of each genotype imbibed in the dark on aqueous agar plates, the hy3 (phyB) mutant did not germinate, whereas the fre1 (phyA) mutant germinated at a rate of 50 to 60%, and the wild type (WT) germinated at a rate of 60 to 70%. By contrast, seeds of all genotypes germinated to nearly 100% when plated in continuous irradiation with white or red light. When plated in continuous far-red light, however, frequencies of seed germination of the WT and the fre1 and hy3 mutants averaged 14, nearly 0, and 47%, respectively, suggesting that PhyB in the red-absorbing form prevents PhyA-dependent germination under continuous far-red light. When irradiated briefly with red or far-red light after imbibition for 1 h, a typical photoreversible effect on seed germination was observed in the fre1 mutant and the WT but not in the hy3 mutant. In contrast, when allowed to imbibe in the dark for 24 to 48 h and exposed to red light, the seed germination frequencies of the hy3 mutant were more than 40%. Immunoblot analyses of the mutant seeds showed that PhyB apoprotein accumulated in dormant seeds of the WT and the fre1 mutant as much as in the seeds that had imbibed. In contrast, PhyA apoprotein, although detected in etiolated seedlings grown in the dark for 5 d, was not detectable in the dormant seeds of the WT and the hy3 mutant. The above physiological and immunochemical evidence indicates that PhyB in the far-red-absorbing form was stored in the Arabidopsis seeds and resulted in germination in the dark. Hence, PhyA does not play any role in dark germination but induces germination under continuous irradiation with far-red light. Finally, we examined seeds from a signal transduction mutant, det1, and a det1/hy3 double mutant. The det1 seeds exhibited photoreversible responses of germination on aqueous agar plates, and the det1/hy3 double mutant seeds did not. Hence, DET1 is likely to act in a distinct pathway from PhyB in the photoregulation of seed germination.
Energy Transfer between Spatially Separated Entangled Molecules

Abstract Light–matter strong coupling allows for the possibility of entangling the wave functions of different molecules through the light field. We hereby present direct evidence of non‐radiative energy transfer well beyond the Förster limit for spatially separated donor and acceptor cyanine dyes strongly coupled to a cavity. The transient dynamics and the static spectra show an energy transfer efficiency approaching 37 % for donor–acceptor distances ≥100 nm. In such systems, the energy transfer process becomes independent of distance as long as the coupling strength is maintained. This is consistent with the entangled and delocalized nature of the polaritonic states.
Implementing true multicast communications support for the JADE/LEAP agent framework

Autonomous agents have proved to be a very adequate paradigm to construct platforms that support mobile computing. However, existing platforms, in the form of middleware or frameworks, have important shortcomings that should be addressed. Consider power consumption in JADE/LEAP, one of the most accepted agent frameworks for devices like PDAs and mobile phones. We describe the design and implementation of a real multicast communication mechanism to support internal group communications in JADE/LEAP, which obviously permits a reduction in the amount of real messages between agents, resulting in power savings. The importance of this work is that we prove our proposal is both effective, because it does not affects the framework performance, and transparent to the application, because the framework's API requires no modifications. Moreover, during the testing of our proposal we found a problem with JADE/LEAP's internal cache. We present a quantitative analysis to assess this problem's impact on performance.
Glycemic Control with Metformin or Insulin Therapy in Adolescents with Type 2 Diabetes Mellitus

BACKGROUND Only metformin and insulin are approved by the FDA for adolescents. OBJECTIVE To study the efficacy of insulin versus metformin in adolescents with type 2 diabetes mellitus (DM2) and examine whether psychosocial factors affect therapeutic efficacy. METHODS Phase I involved a retrospective examination of the medical records of 18 adolescents with DM2. Glycemic control was evaluated by mean HbA1c. We tested for relationships between glycemic control and BMI, number of outpatient visits per year, and self-reported compliance. Phase II employed a pilot questionnaire. RESULTS Glycemic control deteriorated when therapy was changed from insulin (HbA1c, 5.0+/-2.6% [SD]) to metformin (8.4+/-2.9%; p <0.05). Self-reported compliance positively predicted glycemic control (p <0.005) and inversely correlated with degree of weight loss (p <0.05). Pilot questionnaire data suggested that patients may perceive their DM as less serious when treated with metformin. CONCLUSIONS Metformin was often ineffective in our adolescents with DM2 and compliance was a major factor. Altered perception of the seriousness of their DM may have influenced adherence to therapy.
The relationships between trunk function and the findings of transcranial magnetic stimulation among patients with stroke.

In this study, we investigated the relationship between the motor evoked potentials obtained from trunk muscles and the clinical function of trunk muscle. Twenty patients with unilateral hemispheric stroke and 11 healthy adults were examined. The responses of the bilateral external oblique muscles and the erector spinae muscles to the magnetic stimulation of multiple sites over both cortical hemispheres were recorded. Trunk muscle performance was assessed using the Trunk Control Test and Stroke Impairment Assessment Set. In the stroke group, stimulation of the affected hemisphere resulted in a motor evoked potential in only one patient, while the other 19 stroke patients produced no response to stimulation of the affected hemisphere. Stimulation of the unaffected hemisphere evoked bilateral responses in 19 patients. Further, stimulation of the unaffected hemisphere in the stroke group produced larger motor evoked potentials in the ipsilateral muscles than the motor evoked potentials recorded in the ipsilateral muscles of the control group. The clinical assessment scores of trunk function (i.e. Trunk Control Test and trunk items of Stroke Impairment Assessment Set) were correlated with the amplitudes of the motor evoked potentials of the ipsilateral external oblique muscle that were evoked by stimulation of the unaffected hemisphere. Our results suggest that the recovery of trunk function after stroke is associated with an increase in ipsilateral motor evoked potentials in the external oblique muscle upon stimulation of the unaffected hemisphere, suggesting a role for compensatory activation of uncrossed pathways in recovery of trunk function.
Industry, management capabilities and firms' competitiveness: An empirical contribution

The aim of this paper is to contribute to the knowledge of strategic factors that explain the competitive position reached by firms in their activity sector. We have used a survey carried out in 1999 on 287 executives that belong to the service sector in the province of Santa Cruz de Tenerife. We have analysed the differential factors that distinguish the strategic performance of competitive vis-a-vis non-competitive firms, by jointly assessing the variables representative of the sector (five competitive forces defined by Porter) and variables of an internal feature. Finally, we have moved the level of analysis from the industry to the firm; specifically, we have focused on managerial capabilities due to the significant role played by managers in the strategic decision-making process. The use of cluster analysis to classify firms depending on their degree of competitiveness and the application of the See5 induction algorithm of rules and decision trees to determine the differential factors that distinguish competitive from non-competitive firms, provide a methodological framework for the most significant contributions of this work. Copyright © 2004 John Wiley & Sons, Ltd.
An Approach to Domain Transfer in Procedural Content Generation of Two-Dimensional Videogame Levels

Statistical models, such as Markov Chains, have been recently studied in the context of procedural content generation (PCG). These models can capture statistical regularities of a set of training data and use them to sample new content. However, these techniques assume the existence of sufficient training data with which to train the models. In this paper we study the setting in which we might not have enough training data from the target domain, but we have ample training data from another, similar domain. We propose an algorithm to discover a mapping between domains, so that out-of-domain training data can be used to train the statistical model. Specifically, we apply this to two-dimensional level generation, and experiment with three classic video games: Super Mario Bros. , Kid Icarus and Kid Kool.
An Integration of Random Subspace Sampling and Fishervoice for Speaker Verification

In this paper, we propose an integration of random subspace sampling and Fishervoice for speaker veriﬁcation. In the previous random sampling framework [1], we randomly sample the JFA feature space into a set of low-dimensional subspaces. For every random subspace, we use Fishervoice to model the intrinsic vocal characteristics in a discriminant subspace. The complex speaker characteristics are modeled through multiple subspaces. Through a fusion rule, we form a more powerful and stable classiﬁer that can preserve most of the discriminative information. But in many cases, random subspace sampling may discard too much useful discriminative information for high-dimensional feature space. Instead of increasing the number of random subspace or using more complex fusion rules which increase system complexity, we attempt to increase the performance of each individual weak classiﬁer. Hence, we propose to investigate the integration of random subspace sampling with the Fishervoice approach. The proposed new framework is shown to provide better performance in both NIST SRE08 and NIST SRE10 evaluation corpora. Besides, we also apply Probabilistic Linear Discriminant Analysis (PLDA) on the supervector space for comparision. Our proposed framework can improve PLDA performance by a relative decrease of 12.47% in EER and reduced the minDCF from 0.0216 to 0.0210.
Quantitative detection of amyloid-β peptides by mass spectrometry: state of the art and clinical applications

Abstract Alzheimer’s disease (AD) is the most common form of dementia in humans, and a major public health concern with 35 million of patients worldwide. Cerebrospinal fluid (CSF) biomarkers being early diagnostic indicators of AD, it is essential to use the most efficient analytical methods to detect and quantify them accurately. These biomarkers, and more specifically amyloid-β (Aβ) peptides, are measured in routine clinical practice using immunoassays. However, there are several limits to this immunodetection in terms of specificity and multiplexing of the multiple isoforms of the Aβ peptides. To overcome these issues, the quantification of these analytes by mass spectrometry (MS) represents an interesting alternative, and several assays have been described over the past years. This article reviews the different Aβ peptides quantitative MS-based approaches published so far, compares their pre-analytical phase, and the different quantitative strategies implemented that might be suitable for clinical applications.
Inferring nucleosome positions with their histone mark annotation from ChIP data

Motivation: The nucleosome is the basic repeating unit of chromatin. It contains two copies each of the four core histones H2A, H2B, H3 and H4 and about 147 bp of DNA. The residues of the histone proteins are subject to numerous post-translational modifications, such as methylation or acetylation. Chromatin immunoprecipitiation followed by sequencing (ChIP-seq) is a technique that provides genome-wide occupancy data of these modified histone proteins, and it requires appropriate computational methods. Results: We present NucHunter, an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes. NucHunter annotates each of these nucleosomes with the intensities of the histone modifications. We demonstrate that these annotations can be used to infer nucleosomal states with distinct correlations to underlying genomic features and chromatin-related processes, such as transcriptional start sites, enhancers, elongation by RNA polymerase II and chromatin-mediated repression. Thus, NucHunter is a versatile tool that can be used to predict positioned nucleosomes from a panel of histone modification ChIP-seq experiments and infer distinct histone modification patterns associated to different chromatin states. Availability: The software is available at http://epigen.molgen.mpg.de/nuchunter/. Contact: chung@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
MappSent at IJCNLP-2017 Task 5: A Textual Similarity Approach Applied to Multi-choice Question Answering in Examinations

In this paper we present MappSent, a textual similarity approach that we applied to the multi-choice question answering in exams shared task. MappSent has initially been proposed for question-to-question similarity hazem2017. In this work, we present the results of two adaptations of MappSent for the question answering task on the English dataset.
RADIator - An approach for controllable wireless networks

In this paper we propose a novel software-defined networking architecture for enterprise wireless local area networks (WLANs). The goal is to build a framework that exposes tools and methods for a centralized processing of IEEE 802.11 frames. In our architecture all management tasks, including beaconing, client authentication and association, are performed by the central controller instead of the distributed wireless access points as in traditional networks. The generated frames are tunneled to lightweight wireless access points (APs) or thin APs that perform the media access and radio frequency (RF) conversion. Agents executed on thin APs allow scheduling of simple tasks like traffic filtering for local execution. Additionally, the agents provide functions found in modern WLAN chipsets, such as precise frame transmit timings or RF spectrum analysis to the controller. Our architecture allows to delegate computationally intensive tasks to a central instance with enough processing power. Thus, it is best suited for devices with limited resources that we use as thin APs. We present applications that can be built using our framework, e.g., client geolocalization or energy consumption optimization. Finally we evaluate the performance of our architecture in a testbed using COTS devices with open-source software.
Towards diffusion profile image registration

This paper presents a novel method for diffusion MRI registration that treats the diffusion profile as an arbitrary positive-valued function of spatial direction and treats Cartesian diffusion tensors as a special case. A metric based on elementary notions of signal analysis is presented and in the case of diffusion tensors, a closed form expression of the metric is derived in terms of tensor components. The registration method applies piece-wise local affine registration in a multi-resolution framework. Affine registration is defined in terms of an objective function that allows derivatives to be computed analytically. Experimental results demonstrate the robustness of the method for non-linear registration.
Methanogenic burst in the end-Permian carbon cycle

Significance The end-Permian extinction is the most severe biotic crisis in the fossil record. Its occurrence has been attributed to increased CO2 levels deriving from massive Siberian volcanism. However, such arguments have been difficult to justify quantitatively. We propose that the disruption of the carbon cycle resulted from the emergence of a new microbial metabolic pathway that enabled efficient conversion of marine organic carbon to methane. The methanogenic expansion was catalyzed by nickel associated with the volcanic event. We support this hypothesis with an analysis of carbon isotopic changes leading up to the extinction, phylogenetic analysis of methanogenic archaea, and measurements of nickel concentrations in South China sediments. Our results highlight the sensitivity of the Earth system to microbial evolution. The end-Permian extinction is associated with a mysterious disruption to Earth’s carbon cycle. Here we identify causal mechanisms via three observations. First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction. Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation. Collectively, these results are consistent with the instigation of Earth’s greatest mass extinction by a specific microbial innovation.
System Combination for Grammatical Error Correction

Different approaches to high-quality grammatical error correction have been proposed recently, many of which have their own strengths and weaknesses. Most of these approaches are based on classification or statistical machine translation (SMT). In this paper, we propose to combine the output from a classification-based system and an SMT-based system to improve the correction quality. We adopt the system combination technique of Heafield and Lavie (2010). We achieve an F0.5 score of 39.39% on the test set of the CoNLL-2014 shared task, outperforming the best system in the shared task.
Clinical Indicators of Extracranial Carotid Artery Disease in Patients With Transient Symptoms

The clinical findings in 64 patients with transient symptoms of unilateral carotid system ischemic disease (amaurosis fugax or transient focal cerebral ischemic attacks or both) were reviewed in an effort to determine the value of the neurovascular examination in predicting the presence and extent of roentgenographically demonstrated ipsilateral extracranial internal carotid artery disease. Amaurosis fugax seems to be a highly specific indicator of disease, being associated with 4% of normal vessels as compared to 27% for patients with transient focal cerebral ischemic attacks alone. In patients with transient symptoms, the incidence of a normal, ipsilateral carotid artery was 36% in the absence of any positive neurovascular findings, 15% in the presence of an ipsilateral carotid bruit, 6% in the presence of ipsilateral retinal embolic events, 5% in the presence of ipsilateral reduction in superficial temporal or carotid (or both) pulse, 4% in the presence of an ipsilateral reduction in retinal artery pressure, and 3% when more than one of these findings were noted. The neurovascular examination appears to be a useful adjunct in detecting the presence or absence of ipsilateral carotid disease. However, no combination of symptoms or signs would, in all cases, allow one to accurately determine whether a vessel was abnormal, stenotic, or occluded.
The effects of exogenous hormones on genetic tumor formation in Nicotiana hybrids

The effect of exogenous auxin and cytokinin on cell proliferation and differentiation varies with the tissue system, and depends on the endogenous levels of the two hormones in the tissue. In this report, cytokinin (N 6 -benzyladenine, BA) and auxin (indole-3-acetic acid, IAA) were used to treat young seedlings, leaf explants, and genetic tumors of a Nicotiana hybrid. Exogenous BA markedly accelerated genetic tumor formation in young seedlings, while exogenous IAA inhibited it on young seedlings but not on leaf explants. Genetic tumors showed low sensitivity to exogenous BA and IAA. RAPD analysis of the genomes of the genetic tumors and normal tissue suggested that tumor formation is related to genomic instability.
Influence of solar wind energy flux on the interannual variability of ENSO in the subsequent year

Abstract Previous studies have tended to adopt the quasi-decadal variability of the solar cycle (e.g. sunspot number (SSN) or solar radio flux at 10.7 cm (F10.7) to investigate the effect of solar activity on El Niño–Southern Oscillation (ENSO). As one of the major terrestrial energy sources, the effect of solar wind energy flux in Earth’s magnetosphere (Ein) on the climate has not drawn much attention, due to the big challenge associated with its quantitative estimation. Based on a new Ein index estimated by three-dimensional magnetohydrodynamic simulations from a previous study, this study reveals that Ein exhibits both quasi-decadal variability (periodic 11-year) and interannual (2–4 years) variability, which has rarely before been detected by SSN and F10.7. A significant interannual relationship between the annual mean Ein and subsequent early-winter ENSO is further revealed. Following high Ein, the sea level pressure in the subsequent early winter shows significant positive anomalies from Asia southward to the Maritime Continent, and significant negative anomalies over the Southeast and Northeast Pacific, resembling the Southern Oscillation. Meanwhile, significant upper-level anomalous convergence and divergence winds appear over the western and eastern Pacific, which is configured with significant lower-level anomalous divergence and convergence, indicating a weakening of the Walker circulation. Consequently, notable surface easterly wind anomalies prevail over the eastern tropical Pacific, leading to El Niño-like sea surface temperature anomalies. It is suggested that better describing the processes in the solar wind–magnetosphere–ionosphere coupled system is essential to understand the solar influence on climate change.