Miracle-dz/UniFAR-FTUs huggingface dataset:
Oct‐4: a germline‐specific transcription factor mapping to the mouse t‐complex.

Oct‐4 is a maternally expressed octamer‐binding protein encoded by the murine Oct‐4 gene. It is present in unfertilized oocytes, but also in the inner cell mass and in primordial germ cells. Here we show that the ectopic expression of Oct‐4 in HeLa cells is sufficient for transcriptional activation from the octamer motif, indicating that Oct‐4 is a transcription factor. Therefore, Oct‐4 is the first transcription factor described that is specific for the early stages of mouse development. The spatial and temporal expression patterns were further determined using in situ hybridization. With this technique Oct‐4 expression is detected in the oocyte, in the blastocyst and before gastrulation in the embryonic ectoderm. After day 8 Oct‐4 expression decreases and is restricted to primordial germ cells from about day 8.5 onwards. Therefore Oct‐4 is a transcription factor that is specifically expressed in cells participating in the generation of the germline lineage. Linkage analysis using B X D recombinant inbred mouse strains demonstrates that Oct‐4 maps to chromosome 17 in or near the major histocompatibility complex. Several mouse mutants in the distal region of the mouse t‐complex affecting blastocyst and embryonic ectoderm formation also map to this region.
Machine Learning for Language Processing Lecture 1 : Classification

The ML Revolution in NLP The plot on the slide shows the percentage of papers at the main ACL conference which report research on statistical NLP. Today, in 2015, the figure would be close to 100%. Before 1990, research in NLP was rule-based, where the rules were written by domain experts (for example translators, for machine translation). The limitations of rule-based systems are well-documented: large and complex rule sets which are difficult to modify and maintain; expensive human input needed to create the rule sets; and difficulty in adapting rule sets designed for one language domain, e.g. finance, to another, e.g. biomedical text. However, there are advantages to rule-based systems, and it is important to maintain some balance in the debate regarding rule-based vs. statistical. Many commercial NLP systems still use rule-based approaches, for the following reasons. One, they are typically high precision, meaning that, if a rule, or set of rules, does fire, the rule will probably give the right answer; and two, the rules are easy to inspect manually to determine why a system made a particular decision. The second reason is especially valued in the context of safety-criticial systems: if an automatic air traffic control system instructs two planes to land at the same time on the same runway, explaining that ten layers of a deep neural network made the decsision is going to provide little comfort. So why did machine learning take over NLP (and other related disciplines such as speech recognition and computer vision)? The main reason is that ML provides a principled means of learning the required knowledge for intelligent behaviour (assuming we can provide appropriate training data and an appropriate learning objective). The amount of knowledge required is huge, and varies for each domain, so it is unlikely that we could ever solve this problem through hand-written rules.
UvA-DARE (Digital Academic Repository) Experiments in automated support for argument reconstruction

This paper describes the outcomes of experiments in automated support for argument reconstruction from natural language texts. We investigated several possibilities to support a manual process by using natural language processing, from classifying pieces of text as either argumentative or non-argumentative to clustering text fragments in the hope that these clusters would contain similar arguments. Results are diverse, but also show that we cannot come a long way without an extensive pre-tagged corpus.
A note on genetic variance components in mixed models

Burton et al. ([1999] Genet. Epidemiol. 17:118–140) proposed a series of generalized linear mixed models for pedigree data that account for residual correlation between related individuals. These models may be fitted using Markov chain Monte Carlo methods, but the posterior mean for small variance components can exhibit marked positive bias. Burton et al. ([1999] Genet. Epidemiol. 17:118–140) suggested that this problem could be overcome by allowing the variance components to take negative values. We examine this idea in depth, and show that it can be interpreted as a computational device for locating the posterior mode without necessarily implying that the original random effects structure is incorrect. We illustrate the application of this technique to mixed models for familial data. Genet Epidemiol 24:297–301, 2003. © 2003 Wiley‐Liss, Inc.
Compositing User Interfaces in Partitioned In-Vehicle Infotainment

Automotive information and entertainment systems have become an integral part of a car’s human-machine interface and already affect a prospective customer’s purchase decision. In-Vehicle Infotain-ment systems combine an increasing number of software-based functionalities of varying importance and purpose on a shared hardware platform. This led to integrated modular architectures to achieve temporal isolation of different classes of applications, developed independently by multiple suppliers. Despite this partitioning on the software level, the user interface has to provide all functionality in a uniform way, blended into the manufacturer’s superordinate usage concept. Furthermore, allocation and presentation of graphical content has to respect the car’s operating state along with the user’s preferences and system interaction. In the following, an approach is presented that enables the integration of segregated and independently rendered graphics into a uniform graphical user interface, while considering a multi-display environment and flexible allocation of different views. Relevant requirements, a prospective architecture, and a prototypical implementation are presented to foster the provisioning of the required computational and graphical power to enable future In-Vehicle Infotainment systems.
Microfabricated Electrodynamic Synthetic Jet Actuators

This paper presents the design, fabrication, and characterization of a chip-scale electrodynamic synthetic jet actuator with batch-fabricated die components. The actuator is an assembly of two dies with a plastic spacer sandwiched in between. The top die consists of a copper micro-coil and an orifice through which the jet is synthesized. The bottom die consists of a poly-dimethyl-siloxane diaphragm with a wax-bonded NdFeB magnet. When assembled, an ac current applied to the micro-coil forces an oscillatory actuation of the magnet, and correspondingly ingestion and expulsion of fluid through the orifice. The dimensions of the assembled actuator are 7.5 mm <inline-formula> <tex-math notation="LaTeX">$\times7.5$ </tex-math></inline-formula> mm <inline-formula> <tex-math notation="LaTeX">$\times1.1$ </tex-math></inline-formula> mm. The peak jet velocity is measured to be 4.3 m/s at 160 Hz for an input of 200-mA<inline-formula> <tex-math notation="LaTeX">$_{pp}$ </tex-math></inline-formula> current corresponding to 20 mW of input electrical power. [2017-0166]
Flexible Transmission Expansion Planning With Uncertainties in an Electricity Market

Deregulation of the electric power industry has introduced new uncertainties for market participants and made planning of transmission expansion more difficult. More flexible transmission expansion plans are needed, to cope with the increased risks. In this paper, a novel planning approach is proposed to meet the above challenge. In our approach, the planning process is modeled as a mixed integer nonlinear programming (MINLP) problem, so that conflicting objectives can be optimized simultaneously. To minimize planning risks, our method identifies several scenarios based on statistics and expert knowledge; the most flexible expansion plan is selected as the plan that has least adaptation cost. The proposed method is tested with the IEEE 14-bus system. Promising results are obtained to demonstrate the effectiveness of our method.
Fluoroscopically guided scapulothoracic injections.

After informed consent was obtained from the patient, the patient was placed in a prone oblique position on the fluoroscopy table of a C -arm system (Angioskop D 33, Siemens Medical Systems, Erlangen, Germany). The patient was asked to place the arm of the painful side either above the head or at the side of the body to move the scapula away from the chest wall. The choice of arm position depended on which one was more comfortable for the patient and which one best opened the tender area between the scapula and the ribs. The C -arm was rotated until the scapula and the scapulothoracic space were seen in profile. In most patients, the fluoroscopy tube was angled cephalocaudally to profile the anterior and posterior portions of the rib of interest in the same plane, which produced a lordotic view of the ribs. This view helped prevent inadvertent needle puncture of the rib interspace. The patient was asked where the pain was centered while the radiologist palpated medial and deep in relation to the scapula. The site of maximal tenderness was chosen for the
Enhanced gene expression and reduced toxicity in mice using polyplexes of low-molecular-weight poly(ethylene imine) for pulmonary gene delivery

The aim of this study was to elicit improved gene expression and decreased cytotoxicity for pulmonary gene therapy by replacing the commonly used carrier 25 kDa branched poly(ethylene imine) (BPEI) by two PEI derivatives, low-molecular-weight PEI (LMWPEI) and polyethylene glycol−grafted PEI (PEGPEI). All polymers were shown to condense DNA to spherical particles of approximately 100 nm. Biocompatibility was investigated in vitro and in vivo. Although transfection was less efficient with LMWPEI-DNA in vitro, this polyplex caused the highest luciferase expression in the mouse lung after intratracheal instillation. While PEGPEI luciferase expression in vitro was approximately three times higher when compared to BPEI, a transfection rate at the level of naked DNA was observed in vivo. LMWPEI polyplexes were located in both the bronchial and alveolar cells, whereas BPEI polyplexes were mainly detected in bronchial cells. LMWPEI combines low cytotoxicity with high transfection efficiency in the mouse lung in vivo, rendering it a promising strategy for pulmonary gene delivery.
An hardware efficient deblocking filter for H.264/AVC

This work presents an efficient VLSI architecture for the deblocking filter in H.264/AVC standard. The computing flow is reordered for easy hardware implementation. The resulting design can achieve 100 MHz with a gate count of 9.16 K when synthesized from Verilog RTL design by using UMC 0.18 /spl mu/m CMOS technology. When clocked at 82.58 MHz, our design can easily support real-time deblocking of 2K /spl times/ 1K @ 30 Hz video application; this high performance can meet high resolution real-time application requirement.
Functional Outcomes After Open Reduction and Internal Fixation for Treatment of Displaced Distal Radius Fractures in Patients Over 60 Years of Age

Objective: To evaluate the clinical, radiographic, and functional outcomes of patients aged 60 and older treated with open reduction and internal fixation using plates and screws for displaced and comminuted fractures of the distal radius. Design: Retrospective, clinical research. Setting: Tertiary care center (Level 1 trauma center) located in a large urban area. Patients: Eighteen patients with an average age of 71 years (range 60–86) form the basis of this study. Patients were obtained from a surgical database of 2 hand surgeons in a tertiary care center. Intervention: Open reduction and internal fixation of fractures of the distal radius using metal plates and screws designed for treatment of these injuries. Main Outcome Measurements: Clinical (history and physical examination), plain radiographic, and functional assessments were performed at an average follow-up of 26 months (range 12–40 months). Functional outcomes were assessed using the Gartland and Werley and Disabilities of the Arm, Shoulder, and Hand scoring systems. Results: Satisfactory reduction was achieved in all 18 fractures at the time of operative fixation with no instances of loss of fracture reduction during the study period. There were no cases of malunion, nonunion, or instances of device failure. We identified 4 minor complications. No patients required reoperation. Fifteen patients had an excellent (83%) and 3 had a good (17%) result according to the Gartland and Werley scoring system. The mean Disabilities of the Arm, Shoulder, and Hand score was 4.4 (range 0–14) out of a maximum 100. Conclusion: Our findings suggest that open reduction and internal fixation with plates and screws in patients 60 years and older with displaced and comminuted fractures of the distal radius represents a safe and effective treatment alternative.
A relay selection scheme based on the harmonic mean in two-way relay networks with physical layer network coding

In single relay selection is an effective technique to fulfill cooperative communications in two-way relay networks. Previous works took the minimum outage probability as the objective function in relay selection. This paper proposes a single relay selection scheme to maximize the sum rate of the network. The paper establishes the direct relationship between the tight lower bound of the sum rate and the harmonic mean of channel gains. By selecting the maximum harmonic mean among all relay nodes, the scheme maximizes the tight lower bound of the sum rate. Meanwhile, this paper proves that the proposed relay selection scheme could achieve the full diversity order in two-way AF relay networks with physical layer network coding. Simulation results show that the proposed relay selection scheme achieves significant performance improvement over the random selection scheme and performs very close to the optimal selection scheme in the sense of maximum sum rate.
Stability analysis for drugs with multiple active ingredients

For every drug product on the market, the United States Food and Drug Administration (FDA) requires that an expiration dating period (shelf‐life) must be indicated on the immediate container label. For determination of the expiration dating period of a drug product, regulatory requirements and statistical methodology are provided in the FDA and ICH Guidelines. However, this guideline is developed for drug products with a single active ingredient. There are many drug products consisting of multiple active ingredients, especially for most traditional Chinese medicine. In this article, we propose a statistical method for determining the shelf‐life of a drug product with multiple active ingredients following similar idea as suggested by the FDA and assuming that these active ingredients are linear combinations of some factors. Stability data observed from a traditional Chinese medicine were analysed to illustrate the proposed method. Copyright © 2006 John Wiley & Sons, Ltd.
assessment Fear in animals : a meta-analysis and review of risk

Supplementary data ml http://rspb.royalsocietypublishing. org/content/suppl/2009/02/12/272.1581. 2627.DC1. ht "Data Supplement" References http://rspb.royalsocietypublishing. org/content/272/1581/2627.full. html#related-urls Article cited in: http://rspb.royalsocietypublishing. org/content/272/1581/2627.full. html#ref-list-1 This article cites 51 articles, 4 of which can be accessed free Email alerting service here right-hand corner of the article or click Receive free email alerts when new articles cite this article sign up in the box at the top
Synergistic phage-antibiotic combinations for the control of Escherichia coli biofilms in vitro.

The potential application of phage therapy for the control of bacterial biofilms has received increasing attention as resistance to conventional antibiotic agents continues to increase. The present study identifies antimicrobial synergy between bacteriophage T4 and a conventional antibiotic, cefotaxime, via standard plaque assay and, importantly, in the in vitro eradication of biofilms of the T4 host strain Escherichia coli 11303. Phage-antibiotic synergy (PAS) is defined as the phenomenon whereby sub-lethal concentrations of certain antibiotics can substantially stimulate the host bacteria's production of virulent phage. Increasing sub-lethal concentrations of cefotaxime resulted in an observed increase in T4 plaque size and T4 concentration. The application of PAS to the T4 one-step growth curve also resulted in an increased burst size and reduced latent period. Combinations of T4 bacteriophage and cefotaxime significantly enhanced the eradication of bacterial biofilms when compared to treatment with cefotaxime alone. The addition of medium (10(4) PFU mL(-1)) and high (10(7) PFU mL(-1)) phage titres reduced the minimum biofilm eradication concentration value of cefotaxime against E. coli ATCC 11303 biofilms from 256 to 128 and 32 μg mL(-1), respectively. Although further investigation is needed to confirm PAS, this study demonstrates, for the first time, that synergy between bacteriophage and conventional antibiotics can significantly improve biofilm control in vitro.
Combining rotation forests and adaboost for hyperspectral imagery classification using few labeled samples

Classification of hyperspectral imagery using too few labeled samples is a challenging problem considering the high dimensionality of hyperspectral imagery. In this paper, an ensemble method combining rotation forests and AdaBoost is proposed to tackle this problem. By adaptive boosting, AdaBoost can significantly reduce classification error in an iteration compared to a single classifier, and the rotation matrix can increase diversity so that the ensemble performance can be further improved. Experimental resutls show that the final classification accuracy of the proposed algorithm consistently outperforms other state-of-the-art classification methods.
CE‐MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics

Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. CE‐MS, which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enables the diagnosis, classification, and monitoring of a wide range of diseases. CE‐MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level.
The migration of neuroblasts in the developing cerebral cortex.

Tilney (1933) was the first to make a detailed histological study of Nissl-stained preparations of the developing cortex of the rat. He concluded that, after their formation in the ependymal and mantle layers, the neuroblasts migrated to take up definitive positions in the developing cerebrum. He described the cellular migrations as occurring in three distinct waves; the first over the period from the 16th to the 17th day, the second from the 18th to the 19th, and the third from the 20th to the 21st, or last day of gestation, respectively. The neuroblasts involved in the first migration formed a lamina of cells below the pial surface called the 'primary granular lamina' which was later seen to give rise to the two superficial layers of the adult cortex, layers II and III. A 'secondary granular lamina' was described as being formed in a similar manner, by a second migration of cells, and was said to differentiate later into layer IV of the adult cortex. Lastly, the neuroblasts of the third migration established the most deeply situated laminae, layers V and VI. In a study employing an autoradiographic technique in which tritiated thymidine was used, Angevine & Sidman (1961) concluded that the pattern of migration of the neuroblasts of the developing cerebral cortex was the reverse of that proposed by Tilney. Angevine & Sidman found that tritiated thymidine was incorporated into the cells of the ependymal and mantle layers and that the neuroblasts labelled in the early stages of development were later found in the infragranular laminae (layers V and VI), while neuroblasts labelled later subsequently appeared in the granular and supragranular laminate (layers IV, III and II). Berry & Eayrs (1963) studied the teratogenic effects of X-irradiation on the developing cerebral cortex of the rat. Many of the abnormalities they observed were also inconsistent with the sequence of events described by Tilney. For instance, a dose of X-ravs delivered on the 19th day of gestation destroyed the ependymal and mantle layers but left the migrated cells in the more superficial part of the cortex unharmed. On Tilney's hypothesis these surviving cells should later have formed layers II, III and IV of the adult cortex. In fact, quantitative and qualitative examination of the X-irradiated cortices at 30 days post partum showed that layers II, III and IV were almost completely absent, while layers V and VI appeared relatively normal. Like Angevine & Sidman, Berry & Eayrs also concluded that the first neuroblasts to be produced form the infragranular layers, and that the neuroblasts of later divisions must migrate through these laminae to give rise to the more superficial cellular layers of the adult cortex.
Myocardial injection of CA promoter‐based plasmid mediates efficient transgene expression in rat heart

Although naked plasmid injection is the safest and most convenient method for gene delivery, a major limitation of this approach is currently poor transgene expression. The CA promoter (chicken β‐actin promoter with cytomegalovirus, CMV, enhancer) is one of the strongest transcriptional control modules found; however, it is uncertain whether a CA promoter‐based vector is efficient enough for naked gene therapy in a cardiovascular context.
Some Recent Developments in Nonparametric Finance

This paper gives a selective review on some recent developments of nonparametric methods in both continuous and discrete time finance, particularly in the areas of nonparametric estimation and testing of diffusion processes, nonparametric testing of parametric diffusion models, nonparametric pricing of derivatives, nonparametric estimation and hypothesis testing for nonlinear pricing kernel, and nonparametric predictability of asset returns. For each financial context, the paper discusses the suitable statistical concepts, models, and modeling procedures, as well as some of their applications to financial data. Their relative strengths and weaknesses are discussed. Much theoretical and empirical research is needed in this area, and more importantly, the paper points to several aspects that deserve further investigation.