Miracle-dz/UniFAR-FTUs huggingface dataset:
Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1

MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.
Impact of Four Plant Species and Arbuscular Mycorrhizal (AM) Fungi on Polycyclic Aromatic Hydrocarbon (PAH) Dissipation in Spiked Soil

Alfalfa, tall fescue, ryegrass, and celery, some of which were inoculated with the AM fungus Glomus intraradices, were compared for their contributions to phenanthrene (PHE), pyrene (PYR), and dibenzo(a,h)anthracene (DBA) dissipation in spiked soil. A pot experiment was conducted in which PAHs extracted from soil and plant, quantity of PAH degraders, and plant biomass were evaluated. The results showed that biodegradation was the dominant removal mechanism for PAHs from soil while PAH accumulation in the plant tissue was negligible. PAH dissipation varied with the plant species and decreased with the increase of PAH molecular weight. The four plant species displayed a positive effect on PHE dissipation, and alfalfa improved PYR and DBA dissipation. AM fungi significantly increased plant biomass, phosphorus uptake, and PHE removal rate in planted treatments. Plant biomass and PAH degraders showed a weak linear relationship with PAH dissipation, indicating that there might be other important factors influencing PAH dissipation.
Resuscitation of Endovascular Brachytherapy Owing to Improved Logistics

Technology and techniques for minimally invasive endovascular revascularization in patients with peripheral artery disease have rapidly evolved during the last decade, and there is a growing body of experience in the treatment of even complex cases. Endovascular approaches now represent the initial strategy for managing the majority of these mostly polymorbid and therefore high-risk patients. Different technologies, especially stent implantation to resolve the problems of residual stenosis, elastic recoil, and flowlimiting arterial dissection, enable optimization of the primary technical result. However, restenosis has remained, until now, the major drawback of all endovascular techniques. The two primary phenomena that contribute to restenosis after successful angioplasty are chronic vessel constriction (negative remodeling) and neointimal hyperplasia by means of cell proliferation. While stents can reduce acute recoil and the constricting effect of vascular remodeling, they also enhance neointima proliferation within the stent, leading to in-stent stenosis (ISS). Migration of smooth muscle cells through the mesh of the stent and lumen-narrowing proliferation are the hallmarks of ISS. Owing to this, the patency rates of femoropopliteal stenting with the currently available bare nitinol stents are still suboptimal. Increasing knowledge about the pathophysiology of the process leading to restenosis has formerly given the rationale to investigate the potential role of radiation in the prevention of restenosis. Nearly two decades ago, vascular brachytherapy (BT) emerged as a promising, novel technology, with the potential to reduce the rates of restenosis. Different techniques for application of peripheral vascular BT have been studied. Possible technical approaches included external beam radiation with gamma-emitting sources or endovascular BT with radioactive balloons, radioactive stents, high-dose remote gamma radiation, or beta-emitting sources. In the coronary field, vascular BT using beta and gamma irradiation revolutionized the treatment of ISS at that time. In the femoropopliteal segment, centered and noncentered devices with different doses have been applied. Unfortunately, the pivotal trial of BT for the femoral and popliteal arteries using a centering balloon (Paris) catheter with a high dose rate remote afterloader did not show any superior efficacy of radiation over angioplasty alone. To the contrary, several single and multi-institution randomized trials in Europe have demonstrated beneficial short and midterm effects of BT in the femoropopliteal segment in de novo lesions and, especially, in recurrences. BT in peripheral vessels has almost exclusively been based on studies using iridium 192 and high-dose-rate remote afterloader devices to deliver gamma irradiation. Endovascular gamma BT has been applied in dosages of 12, 14, and 18 Gy at a depth of 2 mm into the arterial wall. The cumulative 12month patency in the Vienna-3 trial, using a dose of 18 Gy at 2 mm, seemed superior to the patency achieved in the Vienna-2 trial
Over 12% efficiency Cu2ZnSn(SeS)4 solar cell via hybrid buffer layer

Efficiency of 12.3% on solution-based Cu<sub>2</sub>ZnSn(SeS)<sub>4</sub> (CZTSeS) solar cells was achieved by applying hybrid buffer layer with combination of In-based buffer and Cd-based buffer layers. Previously, the V<sub>oc</sub> boost by the hybrid buffer layer on Cu<sub>2</sub>ZnSnS<sub>4</sub> (CZTS) and CZTSeS solar cells have been reported[1-2]. In this paper, the latest results and some analyses of the hybrid buffer for solution-based CZTSeS cells will be presented.
Loop latency reduction technique for all-digital clock and data recovery circuits

This paper presents an all-digital implemented clock and data recovery circuit. To alleviate the instability contributed by the large latency of digital loop filter, the architecture of two integral paths is proposed in this work. The loop latency from the digital loop filter can be removing by introducing a high speed pre-accumulator cascaded by a low speed accumulator. It increases the phase margin and also improves the loop stability. A smaller proportional gain for the digital loop filter can be chosen without sacrificing the stability. Hence the jitter performance can be improved. The experimental chip occupies a chip area of 0.432mm2 in standard 0.18∧m CMOS technology. It consumes 23.4mW from a 1.8V supply and achieves a peak-to-peak jitter of 0.064 unit interval while operating at the bit rate of 1.25Gb/s.
Child death overview panel: an intensive care retrieval perspective

Childhood obesity is mostly multifactorial, although a proportion of cases have a highly penetrant genetic aetiology. Identifying a genetic cause of childhood obesity can have important implications for patients and relatives. Beckwith–Wiedemann syndrome (BWS) is an overgrowth syndrome with widely variable clinical phenotype that attenuates with age.1 Proposed criteria to warrant its clinical suspicion are the presence of at least three major, or two major plus one minor, features (table 1). Early diagnosis of BWS is relevant because of the increase in risk for malignancies (Wilms tumour and hepatoblastoma). Periodical abdominal ultrasonographic survey and plasma α fetoprotein level determination during infancy and childhood must be done.1 ,2 View this table: Table 1 Clinical features of patients (both females of European ancestry), with respect to the clinical criteria of BWS Various genetic and epigenetic aberrations affecting the imprinted 11p15.5 locus can cause BWS, by downregulation of maternally expressed genes and/or upregulation of paternally expressed genes (figure 1A). 3 The most common defects are the loss of methylation at IC2 (50%), uniparental paternal disomy at 11p15.5 (20%), gain of methylation at IC1 (5%) and point mutations in the maternal allele of CDKN1C . Duplications, inversions or …
An adaptive solution for nonlinear system identification

This paper proposes a new and very simple method to perform identification of nonlinearities in systems that are supposed to be linear. The improvement with respect to the previous approaches lies in the low computational complexity of the solution and the convenient possibility of online evaluation. Simulation results show that the proposed method provides good performance in terms of coefficients identification, resulting in both low steady-state error and high convergence rate of the algorithm, which justifies its applicability in practice.
The Required Written History and Physical is Alive, but Not Entirely Well, in Internal Medicine Clerkships

Background: Effective written communication is a core competency for medical students, but it is unclear whether or how this skill is evaluated in clinical clerkships. Purpose: This study identifies current requirements and practices regarding required written work during internal medicine clerkships. Methods: In 2010, Clerkship Directors of Internal Medicine (CDIM) surveyed its institutional members; one section asked questions about students’ written work. Results were compared to similar, unpublished CDIM 2001 survey questions. Results: Requirements for student-written work were nearly universal (96% in 2001 and 100% in 2010). Only 23% used structured evaluation forms and 16% reported written work was weighted as a percentage of the final grade, although 72% of respondents reported that written work was “factored” into global ratings. Conclusions: Despite near universal requirements for student written work, structured evaluation was not commonly performed, raising concern about the validity of factoring these assessments into grades.
Planning and Problem Solving Skills Following Focal Frontal Brain Lesions in Childhood: Analysis Using the Tower of London

Problem solving skills were investigated in children with focal lesions using the Tower of London test (TOL; Shallice, 1982). The scoring procedure was elaborated from previous studies to delineate separate processes contributing to overall performance in children. Thirty-one children with focal frontal pathology, 18 children with focal pathology in other brain regions (extra-frontal), 17 children with generalized pathology and 38 healthy children participated in the study. Results suggest a distributed network for problem solving skills, particularly cognitive flexibility and goal setting skills. Within the frontal group, children with lesions involving the right pre-frontal cortex had greatest problems with self-regulation, with rule breaks most common among this group. As these skills develop relatively early in comparison to other aspects of executive function, right pre-frontal regions may play a particularly important role in the development of executive skills in childhood, with damage to these regions rendering children vulnerable to a range of cognitive and social deficits.
Reproducibility of T‐Wave Alternans in Congestive Heart Failure: A Theoretical Argument

To the Editor: As of March 30, 2006, there were 320 entries in the PubMed in response to the inquiry phrased as “T-wave alternans” (TWA); however, there were only 10 entries on the “reproducibility of TWA,” and in reality only three of them dealt with reproducibility. In two of these papers, there was evidence that the short-term reproducibility of TWA was good when based on two bicycle tests completed back to back,1 or 4 hours apart.2 One of these studies evaluated patients with congestive heart failure (CHF),1 while the other2 documented high temporal and spatial stability, indicating that TWA was elicited at roughly similar heart rates, involved the same number of ECG leads, and was of reproducible magnitude. In a third study of patients prone to sudden death,3 repetitive baseline assessment of TWA, evaluated by atrial pacing, revealed stability of TWA (9.1 ± 5.8 μV vs 8.5 ± 5.7 μV, P = NS), and reduction with both metoprolol and sotalol. There were no entries in the PubMed in response to the inquiry about “long-term reproducibility of TWA. ” Since medical decisions are often made in response to TWA in patients with CHF, evaluation of the long-term reproducibility of this predicting variable is long overdue. I have observed over the past 8 years significant attenuation of the amplitude of T waves resulting from development of peripheral edema (PEED) of varying etiology4; these changes occur pari passu with attenuation of the amplitude of QRS complexes5 and P waves.6 Similar changes in all these three ECG parameters occur in patients with CHF developing PEED (attenuation), or experiencing alleviation of PEED (augmentation)7 (Fig. 1). One wonders about the effect on the TWA of these attenuations/augmentations of the T waves occurring over days, weeks, or months in patients with CHF. Is the TWA T wave amplitudedependent? This certainly needs to be evaluated in patients with CHF. The matter may be quite
Mapping of Wnt, frizzled, and Wnt inhibitor gene expression domains in the avian otic primordium

Wnt signaling activates at least three different pathways involved in development and disease. Interactions of secreted ligands and inhibitors with cell‐surface receptors result in the activation or regulation of particular downstream intracellular cascades. During the developmental stages of otic vesicle closure and beginning morphogenesis, the forming inner ear transcribes a plethora of Wnt‐related genes. We report expression of 23 genes out of 25 tested in situ hybridization probes on tissue serial sections. Sensory primordia and Frizzled gene expression share domains, with Fzd1 being a continuous marker. Prospective nonsensory domains express Wnts, whose transcripts mainly flank prosensory regions. Finally, Wnt inhibitor domains are superimposed over both prosensory and nonsensory otic regions. Three Wnt antagonists, Dkk1, SFRP2, and Frzb are prominent. Their gene expression patterns partly overlap and change over time, which adds to the diversity of molecular microenvironments. Strikingly, prosensory domains express Wnts transiently. This includes: 1) the prosensory otic region of high proliferation, neuroblast delamination, and programmed cell death at stage 20/21 (Wnt3, ‐5b, ‐7b, ‐8b, ‐9a, and ‐11); and 2) sensory primordia at stage 25 (Wnt7a and Wnt9a). In summary, robust Wnt‐related gene expression shows both spatial and temporal tuning during inner ear development as the otic vesicle initiates morphogenesis and prosensory cell fate determination. J. Comp. Neurol. 517:751–764, 2009. © 2009 Wiley‐Liss, Inc.
A “fluorescence switch” technique increases the sensitivity of proteomic detection and identification of S‐nitrosylated proteins

Protein S‐nitrosylation is a reversible post‐translational modification of protein cysteines that is increasingly being considered as a signal transduction mechanism. The “biotin switch” technique marked the beginning of the study of the S‐nitrosoproteome, based on the specific replacement of the labile S‐nitrosylation by a more stable biotinylation that allowed further detection and purification. However, its application for proteomic studies is limited by its relatively low sensitivity. Thus, typical proteomic experiments require high quantities of protein extracts, which precludes the use of this method in a number of biological settings. We have developed a “fluorescence switch” technique that, when coupled to 2‐DE proteomic methodologies, allows the detection and identification of S‐nitrosylated proteins by using limited amounts of starting material, thus significantly improving the sensitivity. We have applied this methodology to detect proteins that become S‐nitrosylated in endothelial cells when exposed to S‐nitroso‐L‐cysteine, a physiological S‐nitrosothiol, identifying already known S‐nitrosylation targets, as well as proteins that are novel targets. This “fluorescence switch” approach also allowed us to identify several proteins that are denitrosylated by thioredoxin in cytokine‐activated RAW264.7 (murine macrophage) cells. We believe that this method represents an improvement in order to approach the identification of S‐nitrosylated proteins in physiological conditions.
Cloning and sequencing of a cDNA encoding a copper‐zinc superoxide dismutase enzyme from the marine yeast Debaryomyces hansenii

Cu‐Zn superoxide dismutase (SOD‐1) is a ubiquitously occurring eukaryotic enzyme with a variety of important effects on respiring organisms. A gene (dhsod‐1) encoding a Cu‐Zn superoxide dismutase of the marine yeast Debaryomyces hansenii was cloned using mRNA by the RT‐PCR technique. The deduced amino‐acid sequence shows ∼70% homology with that of cytosolic superoxide dismutase from Saccharomyces cerevisiae and Neurospora crassa, as well as lower homologies (between 55 and 65%) with the corresponding enzyme of other eukaryotic organisms, including human. The gene sequence encodes a protein of 153 amino acids with a calculated molecular mass of 15·92 kDa, in agreement with the observed characteristics of the purified protein from D. hansenii. The dhsod‐1 sequence has been deposited in the public data library of the NCBI under Accession Number AFO 16383. © 1998 John Wiley & Sons, Ltd.
Band-gap tailoring of ZnO by means of heavy Al doping.

Films of ZnO:Al were produced by weakly reactive dual-target magnetron sputtering. Optical band gaps, evaluated from spectrophotometric data, were widened in proportion to the Al doping. The widening could be quantitatively reconciled with an effective-mass model for n-doped semiconductors, provided the polar character of ZnO was accounted for.
Early necrosis and apoptosis of Schwann cells transplanted into the injured rat spinal cord

Poor survival of cells transplanted into the CNS is a widespread problem and limits their therapeutic potential. Whereas substantial loss of transplanted cells has been described, the extent of acute cell loss has not been quantified previously. To assess the extent and temporal profile of transplanted cell death, and the contributions of necrosis and apoptosis to this cell death following spinal cord injury, different concentrations of Schwann cells (SCs), lentivirally transduced to express green fluorescent protein (GFP), were transplanted into a 1‐week‐old moderate contusion of the adult rat thoracic spinal cord. In all cases, transplanted cells were present from 10 min to 28 days. There was a 78% reduction in SC number within the first week, with no significant decrease thereafter. Real‐time polymerase chain reaction showed a similar 80% reduction in GFP‐DNA within the first week, confirming that the decrease in SC number was due to death rather than decreased GFP transgene expression. Cells undergoing necrosis and apoptosis were identified using antibodies against the calpain‐mediated fodrin breakdown product and activated caspase 3, respectively, as well as ultrastructurally. Six times more SCs died during the first week after transplantation by necrosis than apoptosis, with the majority of cell death occurring within the first 24 h. The early death of transplanted SCs indicates that factors present, even 1 week after a moderate contusion, are capable of inducing substantial transplanted cell death. Intervention by strategies that limit necrosis and/or apoptosis should be considered for enhancing acute survival of transplanted cells.
Efficient use of execution resources in multicore processor architectures

As the microprocessor industry embraces multicore architectures, inherently parallel applications benefit directly as they easily transform into sets of homogeneous parallel threads. However, many applications do not t this model. These applications include legacy binaries compiled for a single thread of execution and inherently serial applications. The inability of these two kinds of applications to exploit multicore architectures has created a crisis for the microprocessor industry : customers have come to expect significant performance improvements in all of their application every processor generation, but recent multicore architectures have failed to meet those expectations for many applications. This dissertation explores ways in which these applications can run efficiently on multi core platforms. The performance of legacy binaries compiled for a single thread of execution can be improved through automatic parallelization. We introduce a new technique to automatically parallelize binaries as they are executing. The parallelization technique leverages the benefits of hardware transactional memory, a synchronization mechanism enabling optimistic concurrency. Our technique exploits this to parallelize code that a traditional parallelizing compiler would be unable to transform due to potential memory aliasing. Applications with fundamentally serial code can benefits from core customization. The more heterogeneous the cores are, the more likely that a given application will nd a core on which it runs efficiently. We investigate two forms of heterogeneity : that created on homogeneous hardware by unbalanced resource assignment, and heterogeneity created by hardware asymmetry. We first consider a homogeneous multicore system composed of multithreading cores. Often the best schedules on such a system are unbalanced. We propose a set of novel scheduling algorithms that consider unbalanced schedules to nd good application-to-core assignments. We consider objective functions of both performance and energy. We also explore how applications can benefit from diverse Isms by considering heterogeneous-ISA multicore systems. We propose a new technique to rapidly migrate a thread among cores of different Isms, allowing applications to take advantage of hardware heterogeneity for performance gain or energy savings
Opportunistic Spectrum Access with Channel Switching Cost for Cognitive Radio Networks

We study the spectrum access problem in cognitive networks consisting of several frequency channels, each characterized by a channel availability probability due to the activity of the licensed primary users. The key challenge for the unlicensed secondary users to opportunistically access the unused spectrum of the primary users is to learn the channel availabilities and coordinate with others in order to choose the best channels for transmissions without collision in a distributed way. Moreover, due to the drastic cost of changing frequencies in current wireless devices (in terms of delay, packet loss and protocol overhead), an efficient channel access policy should avoid frequently channel switching, unless necessary. We address the spectrum access problem with channel switching cost by developing a block-based distributed channel access policy. Through mathematical analysis, we show that the proposed policy achieves logarithmic regret in spite of the channel switching cost. Extensive simulation studies show that the proposed policy outperforms the solutions in the literature.