Miracle-dz/UniFAR-FTUs huggingface dataset:
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.
Beyond the Randomized Clinical Trial: The Role of Effectiveness Studies in Evaluating Cardiovascular Therapies

Randomized clinical trials (RCTs) are familiar to most clinicians involved in the care of patients with cardiovascular disease. RCTs are the uncontested “gold standard” for establishing causation between a therapy and outcomes for a compelling reason: A large randomized experiment is the only study design that can guarantee that control and intervention subjects are similar in all the known and unknown attributes that influence outcomes.1 In general, RCTs use a rigorous experimental design with the primary goal of understanding the “average” overall benefit and risk of using a standardized therapy in a selected group of patients.2 When well conducted, RCTs have internal validity, and a therapy that is found to have a net biological benefit is considered efficacious.3 Establishing the efficacy of new therapies is critical for advancing medical knowledge. Yet even when an RCT demonstrates substantial net benefit for a specific therapy, its optimal role in routine clinical practice can remain unclear. Concerns frequently relate to how well the therapy may perform in different clinical settings and in broader patient populations than those studied in traditional RCTs. In addition, it is often unclear how therapies are best applied within the larger environment of the healthcare delivery system where costs and availability become issues for patients and clinicians. These concepts, which refer to the external validity of a clinical trial,3 become important as new therapies are applied in real-world settings and are a key focus area for many studies in health services and outcomes research. In contrast to efficacy studies like traditional RCTs, effectiveness studies often require a broader range of methodological tools, which can include both experimental and nonexperimental study designs. In the present article, we review reasons why evidence from traditional RCTs must generally be supplemented by evidence from effectiveness studies to inform best …
In vivo magnetization transfer measurements of experimental spinal cord injury in the rat

Magnetization transfer (MT) imaging techniques were implemented to study a clip compression model of spinal cord injury (SCI) in the rat. The purpose of this study was to determine if the magnetization transfer ratio (MTR) could be used to classify the stage and severity of SCI. Two clip compression injuries were studied: mild SCI and severe SCI. MTRs were determined for gray matter (GM) and white matter (WM) regions and the GM–WM contrast was determined on days 1 and 7 following surgery. Despite differences in pathologic features of mild and severe SCI, the GM–WM contrast did not allow discrimination between the two degrees of severity of SCI. WM MTR allowed differentiation of mild and severe SCI on day 1. These preliminary results suggest that WM MTR may provide an indication of the severity of injury in SCI. Magn Reson Med 45:159–163, 2001. © 2001 Wiley‐Liss, Inc.
Clinical Study Comparison of the Effects of Continuous Subcutaneous Insulin Infusion and Add-on Therapy with Sitagliptin in Patients with Newly Diagnosed Type 2 Diabetes Mellitus

To identify a new regimen to optimize treatment for patients with newly diagnosed type 2 diabetes (T2DM) by short-term continuous subcutaneous insulin infusion (CSII) alone. Methods. 60 patients with newly diagnosed T2DM were randomized into two groups (í µí± = 30 each) and treated for 2 weeks with CSII alone (CSII group) or with CSII plus sitagliptin (CSII + Sig group). The glycemic variability of the patients was measured using a continuous glucose monitoring system (CGMS) for the last 72 hours. A standard meal test was performed before and after the interventions, and the levels of glycated albumin, fasting glucose, fasting C-peptide, postprandial 2 h blood glucose, and postprandial 2 h C-peptide were examined. Results. Compared with the CSII group, the indicators of glycemic variability, such as the mean amplitude of glycemic excursion (MAGE) and the standard deviation of blood glucose (SDBG), were decreased significantly in the CSII + Sig group. The changes before and after treatment in the C-peptide reactivity index (ΔCPI) and the secretory unit of islet in transplantation index (ΔSUIT) indicated a significant improvement in the CSII + Sig group. Conclusions. Add-on therapy with sitagliptin may be an optimized treatment for patients with newly diagnosed T2DM compared with short-term CSII alone.
Fourier Analysis on Motion Using Screw Parameters

In this paper, the author presents the bi-invariant (Haar) integral for the group of rigid-body motions (Euclidean group) in three-dimensional space in terms of finite screw parameters, and proceeds to develop the matrix elements of irreducible unitary representations in this parameterization. This allows one to integrate and expand functions of motion described in terms of screw parameters. In robot kinematics, the screw-parameter description of a finite rigid-body motion is well known. This description of motion in three-dimensional space (which follows from Ball’s work on finite screws) provides an elegant way to view rigid-body kinematics. In contrast, the theoretical physics community usually uses Euler angles and spherical coordinates to parameterize rigid-body motions. It therefore comes as no surprise that in the field of Fourier analysis on groups, which has been developed in large part by theoretical physicists, that the Euler-angle/spherical coordinate description of rigid-body motions is most common. The contribution of this paper is to formulate Fourier analysis on the group of rigid-body motions in terms of screw parameters. The geometrically meaningful nature of the screw parameters combined with the group Fourier transform provides a tool for insight into problems that can be posed as convolutions on the Euclidean group. Such problems include workspace generation of serial linkages, kinematic error propagation, and the statistical mechanics of macromolecules.
Time-optimal path parameterization in SO ( 3 ) with applications to the spacecraft reorientation problem

Time-optimal reorientation of a rigid body is an interesting fundamental problem that arises in a number of applications including spacecraft or robot motion planning, computer animation, etc. There are two main directions of research in the literature. The aerospace community has considered the problem of finding exact time-optimal reorientation trajectories under kinodynamic constraints by applying directly Pontryagin’s minimum principle (Li and Bainum 1990; Bilimoria and Wie 1993; Bai and Junkins 2009). However, this approach could only deal with the relatively simple cases of rest-to-rest motions in an obstacle-free environment. In the robotics community, popular sampling-based motion planning methods such as RRT or PRM have been extended to SO(3)1. Such methods require three components : (i) random sampling, (ii) distance metric, and (iii) interpolation between two points. While straightforward in Euclidean spaces, these three components involve considerable challenges in SO(3). Regarding component (i), a sampling algorithm based on unit quaternions was proposed in (Kuffner 2004). As for components (ii) and (iii), methods based on unit quaternions or on rotation matrices exist, but have rarely been considered in the contexts of kinodynamic constraints and time-optimality. As a result, to our knowledge, there are no general methods for planning fast trajectories in SO(3) under kinodynamic constraints and in a cluttered environment. Here we address this problem by following the widely used plan-andshortcut pipeline, which has shown to be easy to implement, robust and efficient (it is e.g. the default pipeline used in OpenRAVE, a popular robotics software in both academia and industry). This pipeline consists of three steps
Evaluation of record linkage between a large healthcare provider and the Utah Population Database

OBJECTIVE Electronically linked datasets have become an important part of clinical research. Information from multiple sources can be used to identify comorbid conditions and patient outcomes, measure use of healthcare services, and enrich demographic and clinical variables of interest. Innovative approaches for creating research infrastructure beyond a traditional data system are necessary. MATERIALS AND METHODS Records from a large healthcare system's enterprise data warehouse (EDW) were linked to a statewide population database, and a master subject index was created. The authors evaluate the linkage, along with the impact of missing information in EDW records and the coverage of the population database. The makeup of the EDW and population database provides a subset of cancer records that exist in both resources, which allows a cancer-specific evaluation of the linkage. RESULTS About 3.4 million records (60.8%) in the EDW were linked to the population database with a minimum accuracy of 96.3%. It was estimated that approximately 24.8% of target records were absent from the population database, which enabled the effect of the amount and type of information missing from a record on the linkage to be estimated. However, 99% of the records from the oncology data mart linked; they had fewer missing fields and this correlated positively with the number of patient visits. DISCUSSION AND CONCLUSION A general-purpose research infrastructure was created which allows disease-specific cohorts to be identified. The usefulness of creating an index between institutions is that it allows each institution to maintain control and confidentiality of their own information.
Evaluating the effects of Escanbil (Calligonum) extract on the expression level of Catsper gene variants and sperm motility in aging male mice

Background: Catsper proteins are responsible for entering Ca2+ to the cell and play an important role in sperm motility and male fertility. Antioxidants are vital for sperm motility too. Escanbil (Calligonum) extract possess some of the important antioxidant like Catechin and Quercetin. Objective: Here we investigated the effects of Escanbil (Calligonum) extract on the sperm parameters and the expressing of Catsper gene in aging male mice. Materials and Methods: In this animal study, firstly, dose response was performed by using these three doses of Escanbil (Calligonum) (10, 30 and 50 mg/kg). 5 mice in each group were considered and Intra Peritoneal injection was done for 5 weeks. the sperm parameters analyzed and dUTP nick end labeling (TUNEL )staining was done. 30 mg/kg dose was considered as optimum dose. Secondly: fifteen aging male mice (11-13 months) were divided into three groups: control, sham and experiment. The experiments were injected Intra peritonealy with Escanbil (Calligonum) extract (30mg/kg) weekly for up to 5 weeks. The sham group was injected Intra Peritoneal (DMSO). Sperm parameters were analyzed. Expression of Catsper genes was analyzed by Real time PCR. Results: Our results showed that after Escanbil (Calligonum) treatment (30 mg/kg), the sperm parameters were improved in experimental group (p<0.05). Our data showed that there was a statistical significance difference between the expressions of Catsper 2, 4 in aging experiment group comparison with aging control group (p<0.05). Conclusion: We investigated that the Escanbil (Calligonum) extract (30 mg/kg) can improve sperm parameters and change the expression of Catsper genes in aging male mice. This herbal extract can be used as an antioxidant component for clinical usages.
Ocular effects of radiofrequency energy

Radiofrequency (RF) energy has been reported to cause a variety of ocular effects, primarily cataracts but also effects on the retina, cornea, and other ocular systems. Cataracts have been observed in experimental animals when one eye was exposed to a localized, very high RF field and the other eye was the unexposed control. The results show that 2450 MHz exposures for ≥30 min at power densities causing extremely high dose rates (≥150 W/kg) and temperatures (≥41°C) in or near the lens caused cataracts in the rabbit eye. However, cataracts were not observed in the monkey eye exposed to similar exposure conditions, reflecting the different patterns of energy absorption (SAR, specific absorption rate) distribution, due to their different facial structure. Since the monkey head is similar in structure to the human head, the nonhuman primate study showed that the incident power density levels causing cataracts in rabbits and other laboratory animals cannot be directly extrapolated to primates, including human beings. It is reasonable to assume that an SAR that would induce temperatures ≥41°C in or near the lens in the human eye would produce cataracts by the same mechanism (heating) that caused cataracts in the rabbit lens; however, such an exposure would greatly exceed the currently allowable limits for human exposure and would be expected to cause unacceptable effects in other parts of the eye and face. Other ocular effects including corneal lesions, retinal effects, and changes in vascular permeability, have been observed after localized exposure of the eye of laboratory animals to both continuous wave (CW) and pulsed wave (PW) exposures, but the inconsistencies in these results, the failure to independently confirm corneal lesions after CW exposure, the failure to independently confirm retinal effects after PW exposure, and the absence of functional changes in vision are reasons why these ocular effects are not useful in defining an adverse effect level for RF exposure. While cataracts develop after localized exposure of the eye at SARs ≥ 150 W/kg, whole body exposure at much lower levels (14–42 W/kg) is lethal to rabbits. Two studies reported cataracts in this animal after 30 daily exposures at SARs at the upper end of the lethal range, e.g., 38–42 W/kg; however, long term exposure of rabbits (23 h/day, 6 months) at 1.5 W/kg (17 W/kg in the rabbit head) did not cause cataracts or other ocular effects. A long term (1–4 years) investigation of monkeys exposed at high SARs (20 and 40 W/kg to the monkey face) found no cataracts or other ocular effects or change in visual capability. The results of these long term studies support the conclusion that clinically significant ocular effects, including cataracts, have not been confirmed in human populations exposed for long periods of time to low level RF energy. The results of four recent human studies show that there is no clear evidence of an association between RF exposure and ocular cancer. Bioelectromagnetics Supplement 6:S148–S161, 2003. © 2003 Wiley‐Liss, Inc.
Emotion Detection From Infant Facial Expressions And Cries

A new system for translating the infant cries from its facial image and cry sounds is presented in this paper. The system is designed to analyze the facial image and sound of the crying infant to derive the reason why the infant is crying. The image and the sound represent the same cry event. The image processing module determines the state of certain facial features, certain combinations of which determine the reason for crying. The sound processing module analyzes the data for the fundamental frequency and the first two formants and uses k-means clustering to determine the reason of the cry. The decisions from the image and sound processing modules are then fused using a decision level fusion system. The overall accuracy of the image and sound processing modules are 64% and 74.2%, respectively, and that of the fused decision is 75.2%
The Karma of Digg : Reciprocity in Online Social Networks

What motivates participants to donate their time to collective intelligence web sites? We examine the possible mechanisms that drive the website Digg, an online news consolidator in which users help determine the popularity and visibility of stories and other web-based information. Those who submit stories that become popular also actively read and vote for each other’s stories. This behavior can be explained as a form of reciprocity; we show evidence for this and discuss the implications for other communities of practice. Résumé: Que motivent les participants à passer du temps sur des sites web communautaires? Nous étudions les mécanismes du site Digg, un agrégateur de nouvelles dans lequel les utilisateurs déterminent la popularité des histoires. Les rédacteurs des histoires qui deviennent populaires lisent et votent pour les histoires des autres. Ce comportement est une forme de réciprocité.
APPEARANCE-BASED RECOGNITION WITH VARYING PATTERNS

An appearance-based visual recognition system for discrimination between free-form objects is presented. The system has been developed in order to be run in a scene where the number of patterns is considerably large and they are not stable, as new patterns are introduced and others are eliminated along the time. In appearancebased systems, the learning step requires the acquisition of large image sets and an intensive computational cost due to the feature extractors. Generally, learning is performed off-line so computing time is not a problem. However, with varying patterns, learning has to be performed several times and under such circumstances the training time is relevant. The proposed method uses random projection for dimensionality reduction and a k-NN classifier to identify the object correctly. We show that despite the computational simplicity of random projection, it allows to keep enough information of the original appearance-based vectors in order to distinguish between the patterns. Experimental results obtained with several image databases show the validity of the approach.
Iscriminative Learning Has Become a Major Theme in Recent Statistical Signal Processing and Pattern Recognition Research including Practically All Discriminative Learning in Sequential Pattern Recognition

In particular, much of the striking progress in large-scale automatic speech recognition over the past few years has been attributed to the successful development and applications of discriminative learning [35], [38], [47], [48]. A key to understanding the speech process is the dynamic characterization of its sequential-or variable-length pattern. Two central issues in the development of discriminative learning methods for sequential pattern recognition are construction of the objective function for optimization and actual optimization techniques. There have been a wide variety of methods reported in the literature related to both of these issues
Federal Reserve Bank of Dallas Globalization and Monetary Policy Institute the Effect of Trade with Low-income Countries on U.s. Industry Raphael Auer Swiss National Bank 1 Relationship to the Literature 2 Data Description 3 Lic Trade and Factor Intensity

When labor-abundant nations grow, their exports increase more in labor-intensive sectors than in capital-intensive sectors. We utilize this sectoral difference in how exports are affected by growth to identify the causal effect of trade with low-income countries (LICs) on U.S. industry. Our framework relates differences in sectoral inflation rates to differences in comparative advantage-induced import growth rates and abstracts from aggregate fluctuations and sector specific trends. In a panel covering 325 manufacturing industries from 1997 to 2006, we find that LIC exports are associated with strong downward pressure on U.S. producer prices and a large effect on productivity. When LIC exporters capture 1% U.S. market share, producer prices decrease by 3.1%, which is nearly fully accounted by a 2.4% increase in productivity and a 0.4% decrease in markups. We also document that while LICs on average find it easier to penetrate sectors with elastic demand, the price and productivity response to import competition is much stronger in industries with inelastic demand. Overall, between 1997 and 2006, the effect of LIC trade on manufacturing PPI inflation was around two percentage points per year, far too large to be neglected in macroeconomic analysis. for helpful comments and discussions; and Domagoj Arapovic for excellent research assistance. The views in this paper are those of the authors and do not necessarily reflect the views of the Swiss National Bank, the Federal Reserve Bank of Dallas or the Federal Reserve System. China and other poor, yet rapidly growing, nations now account for over a third of global trade and they have a virtual monopoly in specific sectors such as toys and textiles. What is the effect of trade with these low-income countries (LICs) on inflation, productivity, and industry structure in developed economies? The standard approach taken in the literature to identify the causal effect of trade relies on natural experiments, such as one-time tariff reductions. While event studies such as Trefler (2004) have greatly enhanced our understanding of trade's one-time impact, the narrow event window of these experiments limits their ability to capture cumulative effects of a phenomenon such as "globalization. " Moreover, the regime change experiment, due to the paucity of natural events, is not a viable strategy to examine the block impact of trade with the newly developing world. 1 The contribution of this paper is to develop an instrumentation strategy that measures the true effect of the gradual increase in trade with the …
VLGD , Algorithm for Drawing Very Large GraphsMichael GoodrichDept . of Computer

Given a large planar graph we want to display it in a meaningful fashion. We present VLGD: a new, straightforward and fast algorithm for automatic display of very large planar graphs. We recursively divide the graph in pieces of roughly equal size. As a result we get a collection of O(logn) layers, where n is the number of vertices in the graph. Each succeeding layer represents the graph in an increasing level of detail. Each layer is a graph drawn with straight lines and without crossings on the n n grid. VLGD does not rely on any speciic properties of the graph other than planarity. The overall running time of the algorithm is O(n log n).