Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting Expression of Keratins in Mouse and Human Embryonic Stem Cells

RNA expression data reveals that human embryonic stem (hES) cells differ from mouse ES (mES) cells in the expression of RNAs for keratin intermediate filament proteins. These differences were confirmed at the cellular and protein level and may reflect a fundamental difference in the epithelial nature of embryonic stem cells derived from mouse and human blastocysts. Mouse ES cells express very low levels of the simple epithelial keratins K8, K18 and K19. By contrast hES cells express moderate levels of the RNAs for these intermediate filament proteins as do mouse stem cells derived from the mouse epiblast. Expression of K8 and K18 RNAs are correlated with increased c-Jun RNA expression in both mouse and human ES cell cultures. However, decreasing K8 and K18 expression associated with differentiation to neuronal progenitor cells is correlated with increasing expression of the Snai2 (Slug) transcriptional repression and not decreased Jun expression. Increasing K7 expression is correlated with increased CDX2 and decreased Oct4 RNA expression associated with the formation of trophoblast derivatives by hES cells. Our study supports the view that hES cells are more similar to mouse epiblast cells than mouse ES cells and is consistent with the epithelial nature of hES cells. Keratin intermediate filament expression in hES cells may modulate sensitivity to death receptor mediated apoptosis and stress.
Ground-Based Nuclear Explosion Monitoring Technologies 657

The identification of a signature relating depth to a remotely recorded infrasound signal requires a dataset of earthquakes, recorded infrasonically, with well-constrained depths. Although the premise is simple, five significant complications arise: (1) Earthquakes can generate infrasound via a variety of processes, which have occasionally been confused in past studies due to the complexity of the process; (2) mining explosions are efficient infrasound generators and can be mistaken for earthquakes; (3) coherent noise on infrasound arrays can be confused with transient signals; (4) atmospheric path effects must be adequately accounted for; and (5) seismic estimates of depth trade-off with origin time without a measurement in the near-epicentral region. This study provides a comprehensive framework for addressing these limitations, building on a focused study of the Wells, Nevada earthquake sequence that was performed as part of the previous year of this research effort (Arrowsmith et al., 2009). Such an approach is necessary to robustly identify a depth signature within a signal that incorporates various source, path, and receiver effects. In addition, we outline a complementary seismo-acoustic modeling approach, also being explored as part of this study, which should provide insight into the physical basis of an infrasonic depth signature. 2010 Monitoring Research Review: Ground-Based Nuclear Explosion Monitoring Technologies
Two layer channel aware scheduling for QoS support in IEEE 802.16/WiMAX networks

One of the fundamental requirements for IEEE 802.16/WiMAX, to become a key technology for high-speed multimedia service delivery, is QoS (Quality of Service) differentiation. Although different types of QoS classes have been defined by the IEEE 802.16 standard, the scheduling architecture is left to be vendor specific. In this paper, new modifications are purposed, and a detailed simulation study is performed, for different scheduling algorithms which are: RR (Round Robin), WRR (weighted Round Robin) and DRR (Deficit Round Robin). Analysis and evaluation of the performance of each scheduler to support the different QoS classes have been performed. The simulation results show that the purposed channel aware modified DRR scheduler can provide higher service standards to support the QoS in terms of packet loss ratio and bounded delay, which is required by different types of traffic in a time varying channel.
Spiroindolones, a Potent Compound Class for the Treatment of Malaria

Antimalarial Drug Candidate Spiroindolones were discovered as promising antimalarial drug candidates through a high-throughput screening approach that should be applicable to a range of neglected infectious diseases. Rottmann et al. (p. 1175; see the Perspective by Wells) present the preclinical profile for an optimized spiroindolone drug candidate, NITD609. They obtained evidence for a decrease in drug sensitivity in strains of the malaria parasite Plasmodium falciparum bearing amino acid mutations in the P-type ATPase, indicating possible mechanisms of action and/or resistance. High-throughput screening has offered up an oral antimalarial drug and pointers to its mechanism of action. Recent reports of increased tolerance to artemisinin derivatives—the most recently adopted class of antimalarials—have prompted a need for new treatments. The spirotetrahydro-β-carbolines, or spiroindolones, are potent drugs that kill the blood stages of Plasmodium falciparum and Plasmodium vivax clinical isolates at low nanomolar concentration. Spiroindolones rapidly inhibit protein synthesis in P. falciparum, an effect that is ablated in parasites bearing nonsynonymous mutations in the gene encoding the P-type cation-transporter ATPase4 (PfATP4). The optimized spiroindolone NITD609 shows pharmacokinetic properties compatible with once-daily oral dosing and has single-dose efficacy in a rodent malaria model.
Airway Obstruction Is Increased in Pneumocystis-Colonized Human Immunodeficiency Virus-Infected Outpatients

ABSTRACT We investigated the relationship of Pneumocystis colonization, matrix metalloprotease levels in sputum, and airway obstruction in a cohort of human immunodeficiency virus (HIV)-infected outpatients. Pneumocystis-colonized subjects had worse obstruction of airways and higher levels of matrix metalloprotease-12 in sputa, suggesting that Pneumocystis colonization may be important in HIV-associated chronic obstructive pulmonary disease.
Polyphyletic Origin of Pyrrolizidine Alkaloids within the Asteraceae. Evidence from Differential Tissue Expression of Homospermidine Synthase1

The evolution of pathways within plant secondary metabolism has been studied by using the pyrrolizidine alkaloids (PAs) as a model system. PAs are constitutively produced by plants as a defense against herbivores. The occurrence of PAs is restricted to certain unrelated families within the angiosperms. Homospermidine synthase (HSS), the first specific enzyme in the biosynthesis of the necine base moiety of PAs, was originally recruited from deoxyhypusine synthase, an enzyme involved in the posttranslational activation of the eukaryotic initiation factor 5A. Recently, this gene recruitment has been shown to have occurred several times independently within the angiosperms and even twice within the Asteraceae. Here, we demonstrate that, within these two PA-producing tribes of the Asteraceae, namely Senecioneae and Eupatorieae, HSS is expressed differently despite catalyzing the same step in PA biosynthesis. Within Eupatorium cannabinum, HSS is expressed uniformly in all cells of the root cortex parenchyma, but not within the endodermis and exodermis. Within Senecio vernalis, HSS expression has been previously identified in groups of specialized cells of the endodermis and the adjacent root cortex parenchyma. This expression pattern was confirmed for Senecio jacobaea as well. Furthermore, the expression of HSS in E. cannabinum is dependent on the development of the plant, suggesting a close linkage to plant growth.
Relationship between time interval from primary surgery to the start of taxane- plus platinum-based chemotherapy and clinical outcome of patients with advanced epithelial ovarian cancer: results of a multicenter retrospective Italian study.

PURPOSE To assess whether the interval from primary surgery to the start of taxane- plus platinum-based chemotherapy has any impact on the clinical outcome of advanced ovarian cancer patients. PATIENTS AND METHODS The study was conducted on 313 patients who underwent surgery followed by taxane- plus platinum-based chemotherapy. The median follow-up of survivors was 30.7 months (range, 6 to 109 months). RESULTS The 25%, 50%, and 75% quantiles of intervals from surgery to the start of chemotherapy were 11, 21, and 31 days, respectively. After the sixth cycle, 102 patients achieved a pathologic complete response at second-look surgery and 98 obtained a clinical complete response but were not submitted to second-look surgery. Taking into consideration the best assessed response, a complete (either clinical or pathologic) response was found in 200 patients. Residual disease (< or = 1 v > 1 cm; P < .0001) and ascites (absent v present; P = .003) were independent predictive factors for achieving a complete response, whereas residual disease (P = .001) and stage (IIc to III v IV; P = .04) were independent prognostic variables for survival. Conversely, statistical analyses failed to detect significant differences in complete response rates and survival among patients with an interval from surgery to chemotherapy shorter than 11 days, 12 to 21 days, 22 to 31 days, and longer than 31 days. CONCLUSION The interval from surgery to the start of taxane- plus platinum-based chemotherapy seems to have neither a predictive value for response to treatment nor a prognostic relevance for survival of advanced ovarian cancer patients.
Who Can Win a Single-Elimination Tournament?

A single-elimination (SE) tournament is a popular way to select a winner in both sports competitions and in elections. A natural and well-studied question is the tournament fixing problem (TFP): given the set of all pairwise match outcomes, can a tournament organizer rig an SE tournament by adjusting the initial seeding so that their favorite player wins? We prove new sufficient conditions on the pairwise match outcome information and the favorite player, under which there is guaranteed to be a seeding where the player wins the tournament. Our results greatly generalize previous results. We also investigate the relationship between the set of players that can win an SE tournament under some seeding (so called SE winners) and other traditional tournament solutions. In addition, we generalize and strengthen prior work on probabilistic models for generating tournaments. For instance, we show that every player in an n player tournament generated by the Condorcet Random Model will be an SE winner even when the noise is as small as possible, p = Θ(ln n/n); prior work only had such results for p ≥ Ω( ln n/n). We also establish new results for significantly more general generative models.
Deep architectures for Neural Machine Translation

It has been shown that increasing model depth improves the quality of neural machine translation. However, different architectural variants to increase model depth have been proposed, and so far, there has been no thorough comparative study. In this work, we describe and evaluate several existing approaches to introduce depth in neural machine translation. Additionally, we explore novel architectural variants, including deep transition RNNs, and we vary how attention is used in the deep decoder. We introduce a novel "BiDeep" RNN architecture that combines deep transition RNNs and stacked RNNs. Our evaluation is carried out on the English to German WMT news translation dataset, using a single-GPU machine for both training and inference. We find that several of our proposed architectures improve upon existing approaches in terms of speed and translation quality. We obtain best improvements with a BiDeep RNN of combined depth 8, obtaining an average improvement of 1.5 BLEU over a strong shallow baseline. We release our code for ease of adoption.
Quantile smoothing of array CGH data

MOTIVATION Plots of array Comparative Genomic Hybridization (CGH) data often show special patterns: stretches of constant level (copy number) with sharp jumps between them. There can also be much noise. Classic smoothing algorithms do not work well, because they introduce too much rounding. To remedy this, we introduce a fast and effective smoothing algorithm based on penalized quantile regression. It can compute arbitrary quantile curves, but we concentrate on the median to show the trend and the lower and upper quartile curves showing the spread of the data. Two-fold cross-validation is used for optimizing the weight of the penalties. RESULTS Simulated data and a published dataset are used to show the capabilities of the method to detect the segments of changed copy numbers in array CGH data.
The RPT2 Subunit of the 26S Proteasome Directs Complex Assembly, Histone Dynamics, and Gametophyte and Sporophyte Development in Arabidopsis[W]

This study explores the function of two highly conserved isoforms of the Arabidopsis thaliana 26S proteasome subunit RPT2 that participate in proteasome-mediated protein turnover. The data point to a specific role for RPT2 in stem fasciation, male and female gametogenesis, and leaf, root, trichome, and pollen development, along with a common role for RP subunits in histone dynamics and nucleosome assembly. The regulatory particle (RP) of the 26S proteasome contains a heterohexameric ring of AAA-ATPases (RPT1-6) that unfolds and inserts substrates into the core protease (CP) for degradation. Through genetic analysis of the Arabidopsis thaliana gene pair encoding RPT2, we show that this subunit plays a critical role in 26S proteasome assembly, histone dynamics, and plant development. rpt2a rpt2b double null mutants are blocked in both male and female gamete transmission, demonstrating that the subunit is essential. Whereas rpt2b mutants are phenotypically normal, rpt2a mutants display a range of defects, including impaired leaf, root, trichome, and pollen development, delayed flowering, stem fasciation, hypersensitivity to mitomycin C and amino acid analogs, hyposensitivity to the proteasome inhibitor MG132, and decreased 26S complex stability. The rpt2a phenotype can be rescued by both RPT2a and RPT2b, indicative of functional redundancy, but not by RPT2a mutants altered in ATP binding/hydrolysis or missing the C-terminal hydrophobic sequence that docks the RPT ring onto the CP. Many rpt2a phenotypes are shared with mutants lacking the chromatin assembly factor complex CAF1. Like caf1 mutants, plants missing RPT2a or reduced in other RP subunits contain less histones, thus implicating RPT2 specifically, and the 26S proteasome generally, in plant nucleosome assembly.
Quality of stroke rehabilitation clinical practice guidelines.

BACKGROUND AND PURPOSE Clinical practice guidelines (CPGs) are systematically developed statements that assist practitioners to provide appropriate evidence-based care. The purpose of this study was to evaluate the quality of currently published CPGs for stroke care and to examine the reliability and validity of the appraisal of guidelines, research and evaluation (AGREE) instrument. METHODS Multiple databases and Internet resources were searched for stroke care CPGs. Guidelines included were published in English or French from 1998 to 2004 and developed by a group process. Four appraisers evaluated each CPG using the AGREE instrument. The AGREE consists of 23 items, ranked on a 4-point Likert scale, that is organized into six domains. A standardized score is calculated separately for each domain and ranges from 0 to 100. RESULTS Eight guidelines were identified. The AGREE quality scores were high for the 'scope and purpose' domain (mean +/- SE = 71.2 +/- 5.48, intra-class correlation (ICC) = 0.66), and 'clarity and presentation' (mean +/- SE = 70.6 +/- 4.43, ICC = 0.66). There was wide variation in ratings of 'rigour of development' (mean +/- SE = 60.7 +/- 7.1, ICC = 0.75) and 'stakeholder involvement' (mean +/- SE = 52.6 +/- 7.14, ICC = 0.89). The 'editorial independence' (mean +/- SE = 38.1 +/- 8.72, ICC = 0.88) and 'applicability' (mean +/- SE = 35.1 +/- 4.93, ICC = 0.75) had the lowest scores. CONCLUSIONS There is considerable variability in quality of stroke care guidelines but stroke guidelines score higher on the AGREE rigour of development domain than CPGs from other medical fields. The Scottish Intercollegiate Guideline Network, Veterans Affairs/Department of Defence, Royal College of Physicians, and the New Zealand Guidelines Group consistently scored the highest across the domains. Stroke rehabilitation clinicians should consider these results in selecting a guideline. CPG development groups can improve their AGREE scores by considering the cost of implementing their CPGs, pilot testing their CPGs, recording conflict of interest of development panel members and providing tools supporting application of their CPGs.
A Fully Pipelined FPGA Architecture of a Factored Restricted Boltzmann Machine Artificial Neural Network

Artificial neural networks (ANNs) are a natural target for hardware acceleration by FPGAs and GPGPUs because commercial-scale applications can require days to weeks to train using CPUs, and the algorithms are highly parallelizable. Previous work on FPGAs has shown how hardware parallelism can be used to accelerate a “Restricted Boltzmann Machine” (RBM) ANN algorithm, and how to distribute computation across multiple FPGAs. Here we describe a fully pipelined parallel architecture that exploits “mini-batch” training (combining many input cases to compute each set of weight updates) to further accelerate ANN training. We implement on an FPGA, for the first time to our knowledge, a more powerful variant of the basic RBM, the “Factored RBM” (fRBM). The fRBM has proved valuable in learning transformations and in discovering features that are present across multiple types of input. We obtain (in simulation) a 100-fold acceleration (vs. CPU software) for an fRBM having N = 256 units in each of its four groups (two input, one output, one intermediate group of units) running on a Virtex-6 LX760 FPGA. Many of the architectural features we implement are applicable not only to fRBMs, but to basic RBMs and other ANN algorithms more broadly.
Online visual object tracking with supervised sparse representation and learning

In this paper, an online visual object tracking algorithm based on the discriminative sparse representation framework with supervised learning is proposed. Different from the generative sparse representation based tracking algorithms, the proposed method casts the tracking problem into a binary classification task. A linear classifier is embedded into the sparse representation model by incorporating the classification error into the objective function to achieve discriminative classification. The dictionary and the classifier are jointly trained using the online dictionary learning algorithm, thus allow the model can adapt the dynamic variations of target appearance and background environment. The target locations are updated based on the classification score and the greedy search motion model. The proposed method is evaluated using four benchmark datasets and is compared with three state-of-the-art tracking algorithms. The results show that the discriminative sparse representation facilitates the tracking performance.
Temperature-Induced Changes in the Lipopolysaccharide of Yersinia pestis Affect Plasminogen Activation by the Pla Surface Protease

ABSTRACT The Pla surface protease of Yersinia pestis activates human plasminogen and is a central virulence factor in bubonic and pneumonic plague. Pla is a transmembrane β-barrel protein and member of the omptin family of outer membrane proteases which require bound lipopolysaccharide (LPS) to be proteolytically active. Plasminogen activation and autoprocessing of Pla were dramatically higher in Y. pestis cells grown at 37°C than in cells grown at 20°C; the difference in enzymatic activity by far exceeded the increase in the cellular content of the Pla protein. Y. pestis modifies its LPS structure in response to growth temperature. We purified His6-Pla under denaturing conditions and compared various LPS types for their capacity to enhance plasmin formation by His6-Pla solubilized in detergent. Reactivation of His6-Pla was higher with Y. pestis LPSs isolated from bacteria grown at 37°C than with LPSs from cells grown at 25°C. Lack of O antigens and the presence of the outer core region as well as a lowered level of acylation in LPS were found to enhance the Pla-LPS interaction. Genetic substitution of arginine 138, which is part of a three-dimensional protein motif for binding to lipid A phosphates, decreased both the enzymatic activity of His6-Pla and the amount of Pla in Y. pestis cells, suggesting the importance of the Pla-lipid A phosphate interaction. The temperature-induced changes in LPS are known to help Y. pestis to avoid innate immune responses, and our results strongly suggest that they also potentiate Pla-mediated proteolysis.
Cadaveric study of movement in the unstable upper cervical spine during emergency management: tracheal intubation and cervical spine immobilisation—a study protocol for a prospective randomised crossover trial

Introduction Emergency management of upper cervical spine injuries often requires cervical spine immobilisation and some critical patients also require airway management. The movement of cervical spine created by tracheal intubation and cervical spine immobilisation can potentially exacerbate cervical spinal cord injury. However, the evidence that previous studies have provided remains unclear, due to lack of a direct measurement technique for dural sac's space during dynamic processes. Our study will use myelography method and a wireless human motion tracker to characterise and compare the change of dural sac's space during tracheal intubations and cervical spine immobilisation in the presence of unstable upper cervical spine injury such as atlanto-occipital dislocation or type II odontoid fracture. Methods and analysis Perform laryngoscopy and intubation, video laryngoscope intubation, laryngeal tube insertion, fiberoptic intubation and cervical collar application on cadaveric models of unstable upper cervical spine injury such as atlanto-occipital dislocation or type II odontoid fracture. The change of dural sac's space and the motion of unstable cervical segment are recorded by video fluoroscopy with previously performing myelography, which enables us to directly measure dural sac's space. Simultaneously, the whole cervical spine motion is recorded at a wireless human motion tracker. The maximum dural sac compression and the maximum angulation and distraction of the injured segment are measured by reviewing fluoroscopic and myelography images. Ethics and dissemination This study protocol has been approved by the Ethics Committee of the State Medical Association Rhineland-Palatinate, Mainz, Germany. The results will be published in relevant emergency journals and presented at relevant conferences. Trial registration number DRKS00010499.