LLukas22/scidocs huggingface dataset:
TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice.

Here we present TENOR (Transcriptome ENcyclopedia Of Rice, http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNA sequencing (mRNA-Seq) data obtained from rice under a wide variety of conditions. Since the elucidation of the ability of plants to adapt to various growing conditions is a key issue in plant sciences, it is of great interest to understand the regulatory networks of genes responsible for environmental changes. We used mRNA-Seq and performed a time-course transcriptome analysis of rice, Oryza sativa L. (cv. Nipponbare), under 10 abiotic stress conditions (high salinity; high and low phosphate; high, low and extremely low cadmium; drought; osmotic; cold; and flood) and two plant hormone treatment conditions (ABA and jasmonic acid). A large number of genes that were responsive to abiotic stresses and plant hormones were detected by differential expression analysis. Furthermore, several responsive genes were found to encode transcription factors that could control the transcriptional network of stress responses, but the timing of the induction of these genes was not uniform across conditions. A significant number of cis-regulatory elements were enriched in the promoter regions of the responsive genes and were shared among conditions. These data suggest that some key components of gene regulation networks are shared between different stress signaling pathways. All the resources (novel genes identified from mRNA-Seq data, expression profiles, co-expressed genes and cis-regulatory elements) can be searched for and are available in TENOR.
News Recommendations from Social Media Opinion Leaders: Effects on Media Trust and Information Seeking

Polls show a strong decline in public trust of traditional news outlets; however, social media offers new avenues for receiving news content. This experiment used the Facebook API to manipulate whether a news story appeared to have been posted on Facebook by one of the respondent’s real-life Facebook friends. Results show that social media recommendations improve levels of media trust, and also make people want to follow more news from that particular media outlet in the future. Moreover, these effects are amplified when the real-life friend sharing the story on social media is perceived as an opinion leader. Implications for democracy and the news business are discussed.
Nanoscale assembly processes revealed in the nacroprismatic transition zone of Pinna nobilis mollusc shells

Intricate biomineralization processes in molluscs engineer hierarchical structures with meso-, nano- and atomic architectures that give the final composite material exceptional mechanical strength and optical iridescence on the macroscale. This multiscale biological assembly inspires new synthetic routes to complex materials. Our investigation of the prism-nacre interface reveals nanoscale details governing the onset of nacre formation using high-resolution scanning transmission electron microscopy. A wedge-polishing technique provides unprecedented, large-area specimens required to span the entire interface. Within this region, we find a transition from nanofibrillar aggregation to irregular early-nacre layers, to well-ordered mature nacre suggesting the assembly process is driven by aggregation of nanoparticles (∼50-80 nm) within an organic matrix that arrange in fibre-like polycrystalline configurations. The particle number increases successively and, when critical packing is reached, they merge into early-nacre platelets. These results give new insights into nacre formation and particle-accretion mechanisms that may be common to many calcareous biominerals.
Recursive three-dimensional model reconstruction based on Kalman filtering

A recursive two-step method to recover structure and motion from image sequences based on Kalman filtering is described in this paper. The algorithm consists of two major steps. The first step is an extended Kalman filter (EKF) for the estimation of the object's pose. The second step is a set of EKFs, one for each model point, for the refinement of the positions of the model features in the three-dimensional (3-D) space. These two steps alternate from frame to frame. The initial model converges to the final structure as the image sequence is scanned sequentially. The performance of the algorithm is demonstrated with both synthetic data and real-world objects. Analytical and empirical comparisons are made among our approach, the interleaved bundle adjustment method, and the Kalman filtering-based recursive algorithm by Azarbayejani and Pentland. Our approach outperformed the other two algorithms in terms of computation speed without loss in the quality of model reconstruction.
Social norms and energy conservation

This paper evaluates a series of programs, run by a company called OPOWER, to send Home Energy Report letters to residential utility customers comparing their energy use to that of their neighbors. Using data from randomized natural eld experiments at 600,000 treatment and control households across the United States, I estimate that the programs reduce energy consumption by 1.1 to 2.8 percent relative to baseline. The program provides additional evidence that non-price interventions can substantially and cost e¤ectively change consumer behavior: the e¤ect is equivalent to that of a short-run electricity price increase of 17 to 28 percent, and the cost e¤ectiveness compares favorably to that of traditional energy conservation programs. I show that there is substantial treatment e¤ect heterogeneity and implement an optimal variable selection algorithm to illustrate how "proling," or using a statistical decision rule to target the program at households with higher expected Conditional Average Treatment E¤ects, could further improve cost e¤ectiveness by 43 percent. JEL Codes: C44, D12, L94, Q41. Keywords: Social norms, energy demand, randomized eld experiments, proling.                             I thank, without implicating, Ian Ayres, Bob Cialdini, Tyler Curtis, Rajeev Dehejia, Kenneth Gillingham, Larry Goulder, Michael Greenstone, Matt Harding, Kosuke Imai, Seema Jayachandran, Karthik Kalyanaraman, Alex Kaufman, Ogi Kavazovic, Alex Laskey, Aprajit Mahajan, Sendhil Mullainathan, Dave Rapson, Todd Rogers, Eldar Shar, Joe Shapiro, Lan Shi, Marc Solomon, Dmitry Taubinsky, and seminar participants at Harvard, Stanford, and the Environmental Defense Fund for helpful conversations related to this project. This is a revision of the original July 2009 working paper (Allcott 2009).
Learning Semantic Similarity

The standard representation of text documents as bags of words suffers from well known limitations, mostly due to its inability to exploit semantic similarity between terms. Attempts to incorporate some notion of term similarity include latent semantic indexing [8], the use of semantic networks [9], and probabilistic methods [5]. In this paper we propose two methods for inferring such similarity from a corpus. The first one defines word-similarity based on document-similarity and viceversa, giving rise to a system of equations whose equilibrium point we use to obtain a semantic similarity measure. The second method models semantic relations by means of a diffusion process on a graph defined by lexicon and co-occurrence information. Both approaches produce valid kernel functions parametrised by a real number. The paper shows how the alignment measure can be used to successfully perform model selection over this parameter. Combined with the use of support vector machines we obtain positive results.
The diameter of the world wide web

The diameter of the world wide web Despite its increasing role in communication, the world wide web (www) remains the least controlled medium: any individual or institution can create websites with unrestricted number of documents and links. This unregulated growth leads to a huge and complex web, which is a large directed graph, whose vertices are documents and edges are the links (URLs) pointing from one document to another. The topology of this graph determines the web's connectivity and, consequently, our effectiveness in locating information on the www. However, due to its large size (estimated to be at least 8 × 10 8 documents [1]), and the continuously changing documents and links, it is impossible to catalogue all vertices and edges. The challenge in obtaining a complete topological map of the www is illustrated by the limitations of the commercial search engines: Northern Light, the search engine with the largest coverage, is estimated to index only 38% of the web [1]. While great efforts are made to map and characterize the Internet's infrastructure [2], little is known about what truly matters in searching for information, i.e., about the topology of the www. Here we take a first step to fill this gap: we use local connectivity measurements to construct a topological model of the www, allowing us to explore and characterize the large scale properties of the web. To determine the local connectivity of the www, we constructed a robot, that adds to its database all URLs found on a document and recursively follows these to retrieve the related documents and URLs. From the collected data we determined the probability P out (k) (P in (k)) that a document has k outgoing (incoming) links. As Figs. 1a and b illustrate, we find that both P out (k) and P in (k) follow a power-law over several orders of magnitude, remarkably different not only from the Poisson distribution predicted by the classical theory of random graphs by Erd˝ os and Rényi [3,4], but also from the bounded distribution found in recent models of random networks [5]. The power law tail indicates that the probability of finding documents with a large number of links is rather significant, the network connectivity 1
Penis deformity after intra-urethral liquid paraffin administration in a young male: a case report

BACKGROUND
Self-induced injections of liquid substances mainly for penis enlargement is a well-documented but still rather uncommon practice in the western world.


CASE PRESENTATION
Herein we present the case of a 30-year-old male who self-inflicted, twice in a six-month-period, intra-urethral liquid paraffin and tied up his penis with a cord in order to achieve both enlargement and elongation. He arrived in our emergency department suffering from suprapubic pain; physical examination revealed a rather unique deformity of the penis. He finally refused any treatment and absconded.


CONCLUSION
Side effects after paraffin administration are various and sometimes severe. Most of the times surgical treatment is needed and radical excision together with follow-up seems the best modality. Such practices emphasize on the public's misbelieves and that some aspects of sexual medicine are yet covered with the veil of misconception.
Digital droplets: Microsoft SkyDrive forensic data remnants

Cloud storage services such as the popular Microsoft© SkyDrive© provide both organisational and individual users a cost-effective, and in some cases free, way of accessing, storing and disseminating data. The identification of digital evidence relating to cloud storage services can, however, be a challenge in a digital forensic investigation. Using SkyDrive as a case study,we identified the types of terrestrial artefacts that are likely to remain on a client’s machine (in the context of our experiments; computer hard drive and iPhone), and where the access point(s) for digital forensics examiners are, that will allow them to undertake steps to secure evidence in a timely fashion. © 2013 Elsevier B.V. All rights reserved.
[Prenatal and clinicopathological study of 6 cases of Pallister-Killian syndrome and review].

OBJECTIVE
In multidisciplinary prenatal diagnosis centers, the search for a tetrasomy 12p mosaic is requested following the discovery of a diaphragmatic hernia in the antenatal period. Thus, the series of Pallister Killian syndromes (PKS: OMIM 601803) probably overestimate the prevalence of diaphragmatic hernia in this syndrome to the detriment of other morphological abnormalities.


METHODS
A multicenter retrospective study was conducted with search for assistance from members of the French society for Fetal Pathology. For each identified case, we collected all antenatal and postnatal data. Antenatal data were compared with data from the clinicopathological examination to assess the adequacy of sonographic signs of PKS. A review of the literature on antenatal morphological anomalies in case of PKS completed the study.


RESULTS
Ten cases were referred to us: 7 had cytogenetic confirmation and 6 had ultrasound screening. In the prenatal as well as post mortem period, the most common sign is facial dysmorphism (5 cases/6). A malformation of limbs is reported in half of the cases (3 out of 6). Ultrasound examination detected craniofacial dysmorphism in 5 cases out of 6. We found 1 case of left diaphragmatic hernia. Our results are in agreement with the malformation spectrum described in the literature.


CONCLUSION
Some malformation associations could evoke a SPK without classical diaphragmatic hernia.
C-LEARN: Learning geometric constraints from demonstrations for multi-step manipulation in shared autonomy

Learning from demonstrations has been shown to be a successful method for non-experts to teach manipulation tasks to robots. These methods typically build generative models from demonstrations and then use regression to reproduce skills. However, this approach has limitations to capture hard geometric constraints imposed by the task. On the other hand, while sampling and optimization-based motion planners exist that reason about geometric constraints, these are typically carefully hand-crafted by an expert. To address this technical gap, we contribute with C-LEARN, a method that learns multi-step manipulation tasks from demonstrations as a sequence of keyframes and a set of geometric constraints. The system builds a knowledge base for reaching and grasping objects, which is then leveraged to learn multi-step tasks from a single demonstration. C-LEARN supports multi-step tasks with multiple end effectors; reasons about SE(3) volumetric and CAD constraints, such as the need for two axes to be parallel; and offers a principled way to transfer skills between robots with different kinematics. We embed the execution of the learned tasks within a shared autonomy framework, and evaluate our approach by analyzing the success rate when performing physical tasks with a dual-arm Optimas robot, comparing the contribution of different constraints models, and demonstrating the ability of C-LEARN to transfer learned tasks by performing them with a legged dual-arm Atlas robot in simulation.
Antibiotic use in acute pancreatitis: An audit of current practice in a tertiary centre.

INTRODUCTION
Intravenous antibiotic prophylaxis is not recommended in acute pancreatitis. According to current international guidelines antibiotics together with further intervention should be considered in the setting of infected necrosis. Appropriate antibiotic therapy particularly avoiding over-prescription is important. This study examines antibiotic use in acute pancreatitis in a tertiary centre using the current IAP/APA guidelines for reference.


METHODS
Data were collected on a consecutive series of patients admitted with acute pancreatitis over a 12 month period. Data were dichotomized by patients admitted directly to the centre and tertiary transfers. Information was collected on clinical course with specific reference to antibiotic use, episode severity, intervention and outcome.


RESULTS
111 consecutive episodes of acute pancreatitis constitute the reported population. 31 (28%) were tertiary transfers. Overall 65 (58.5%) patients received antibiotics. Significantly more tertiary transfer patients received antibiotics. Mean person-days of antibiotic use was 23.9 (sd 29.7) days in the overall study group but there was significantly more use in the tertiary transfer group as compared to patients having their index admission to the centre (40.9 sd 37.1 vs 10.2 sd 8.9; P < 0.005). Thirty four (44%) of patients with clinically mild acute pancreatitis received antibiotics.


CONCLUSIONS
There is substantial use of antibiotics in acute pancreatitis, in particular in patients with severe disease. Over-use is seen in mild acute pancreatitis. Better consideration must be given to identification of prophylaxis or therapy as indication. In relation to repeated courses of antibiotics in severe disease there must be clear indications for use.
Surgical treatment for congestive heart failure with autologous adult stem cell transplantation: a prospective randomized study.

BACKGROUND
Autologous adult stem cell transplantation has been touted as the latest tool in regenerative medical therapy. Its potential for use in cardiovascular disease has only recently been recognized. A randomized study was conducted with a novel epicardial technique to deploy stem cells as an adjuvant to conventional revascularization therapy in patients with congestive heart failure.


METHODS
After institutional review board and government approval, adult autologous stem cell transplantation (CD34+) was performed in patients with ischemic cardiomyopathy and an ejection fraction of less than 35% who were scheduled for primary off-pump coronary artery bypass grafting. Preoperatively, the patients underwent echocardiography, stress thallium imaging single photon emission computed tomography, and cardiac catheterization to identify ischemic regions of the heart and to guide in the selection of stem cell injection sites. The patients were prospectively randomized before the operative therapy was performed. Patient follow-up was 1, 3, and 6 months with echocardiography, single photon emission computed tomography, and angiography.


RESULTS
There were 20 patients enrolled in the study. Ten patients had successful subepicardial transplantation of autologous stem cells into ischemic myocardium. The other 10 patients, the control group, only had off-pump coronary artery bypass grafting. There were 8 male and 2 female subjects in each group. The median number of grafts performed was 1 in both groups. On angiographic follow-up, all grafts were patent at 6 months. The ejection fractions of the off-pump coronary artery bypass grafting group versus the off-pump coronary artery bypass grafting plus stem cell transplantation group were as follows: preoperative, 30.7% +/- 2.5% versus 29.4% +/- 3.6%; 1 month, 36.4% +/- 2.6% versus 42.1% +/- 3.5%; 3 months, 36.5% +/- 3.0% versus 45.5% +/- 2.2%; and 6 months, 37.2% +/- 3.4% versus 46.1% +/- 1.9% (P < .001). There were no perioperative arrhythmias or neurologic or ischemic myocardial events in either group.


CONCLUSIONS
Autologous stem cell transplantation led to significant improvement in cardiac function in patients undergoing off-pump coronary artery bypass grafting for ischemic cardiomyopathy. Further investigation is required to quantify the optimal timing and specific cellular effects of the therapy.
Small-Size Loop Antenna With a Parasitic Shorted Strip Monopole for Internal WWAN Notebook Computer Antenna

A simple meandered loop antenna with a parasitic shorted strip monopole, both printed on a thin dielectric substrate and folded to occupy a small size of 50 × 10 × 4 mm3, for the internal penta-band WWAN notebook computer antenna is presented. The antenna can provide two wide operating bands to cover the GSM850/900 operation (824-960 MHz) and the GSM1800/1900/UMTS (1710-2170 MHz) operation. The lower band is formed by two resonant modes, one half-wavelength loop mode contributed by the meandered loop and one quarter- wavelength monopole mode contributed by the parasitic shorted strip. The upper band is mainly formed by two higher-order loop resonant modes, with their good impedance matching obtained owing to the parasitic shorted strip. Further, in order to decrease the effects of the display ground and keyboard ground of the notebook computer on the antenna performances, two linear slits are embedded in the keyboard ground near the two connection hinges between the two grounds. The two linear slits function as current traps and can effectively reduce the excited surface currents on the keyboard ground. This leads to decreasing size of the effective notebook computer ground plane seen by the antenna. Thus, degrading ground plane effect on the performances of the internal WWAN antenna can be greatly reduced.
Yield Strength Ratio and Liquefaction Analysis of Slopes and Embankments

A procedure is proposed to evaluate the triggering of liquefaction in ground subjected to a static shear stress, i.e., sloping ground, using the yield strength ratio, su(yield)/ v0 . Thirty liquefaction flow failures were back analyzed to evaluate shear strengths and strength ratios mobilized at the triggering of liquefaction. Strength ratios mobilized during the static liquefaction flow failures ranged from approximately 0.24 to 0.30 and are correlated to corrected cone and standard penetration resistances. These yield strength ratios and previously published liquefied strength ratios are used to develop a comprehensive liquefaction analysis for ground subjected to a static shear stress. This analysis addresses: 1 liquefaction susceptibility; 2 liquefaction triggering; and 3 post-triggering/flow failure stability. In particular, step 2 uses the yield strength ratio back-calculated from flow failure case histories and the cyclic stress method to incorporate seismic loading. DOI: 10.1061/ ASCE 1090-0241 2003 129:8 727 CE Database subject headings: Liquefaction; Slopes; Embankments; Shear strength.
Online Estimation of Ship Dynamic Flexure Model Parameters for Transfer Alignment

This paper presents an online approach for estimating the dynamic flexure model parameters in shipboard transfer alignment (TA). Traditionally, the application of Kalman filters (KFs) to the TA process is often restricted because of the lack of real-time information on dynamic flexure characteristics, and a KF designed on the basis of inaccurate parameters of the dynamic flexure model will result in a large alignment error. To overcome this difficulty, a parameter estimation algorithm is proposed in this paper, which utilizes the angular increment difference measured by the master inertial navigation system (MINS) and the slave inertial navigation system. Specifically, the Tufts-Kumaresan method is introduced to compute the unknown parameters of the dynamic flexure model from the angular increment correlation function. Our simulation results show that the proposed method can estimate the dynamic flexure parameters with a high degree of accuracy, even in low signal-to-noise ratio conditions. This parameter estimation method does not require a priori knowledge of dynamic flexure characteristics and, therefore, provides the shipboard sensors with an accurate and rapid-response capability for alignment with the MINS.
Neural Coreference Resolution with Deep Biaffine Attention by Joint Mention Detection and Mention Clustering

Mention Detection Analysis In Table 1, we compare our model with previous state-of-the-art systems on the CoNLL-2012 Shared Task English data. We obtain the best results in all F1 metrics. Our single model achieves 67.8% F1 and our 5-model ensemble achieves 69.2% F1. In particular, compared with Lee et al. (2017), our improvement mainly results from the precision scores. This indicates that the mention detection loss does produce better mention scores and the biaffine attention more effectively determines if two spans are coreferent. Rui Zhang1, Cicero Nogueira dos Santos2, Michihiro Yasunaga1, Bing Xiang2, Dragomir Radev1 Neural Coreference Resolution with Deep Biaffine Attention by Joint Mention Detection and Mention Clustering