Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative genomics and the study of evolution by natural selection

Genomics profoundly affects most areas of biology, including ecology and evolutionary biology. By examining genome sequences from multiple species, comparative genomics offers new insight into genome evolution and the way natural selection moulds DNA sequence evolution. Functional divergence, as manifested in the accumulation of nonsynonymous substitutions in protein‐coding genes, differs among lineages in a manner seemingly related to population size. For example, the ratio of nonsynonymous to synonymous substitution (dN/dS) is higher in apes than in rodents, compatible with Ohta's nearly neutral theory of molecular evolution, which suggests that the fixation of slightly deleterious mutations contributes to protein evolution at an extent negatively correlated with effective population size. While this supports the idea that functional evolution is not necessarily adaptive, comparative genomics is uncovering a role for positive Darwinian selection in 10–40% of all genes in different lineages, estimates that are likely to increase when the addition of more genomes gives increased power. Again, population size seems to matter also in this context, with a higher proportion of fixed amino acid changes representing advantageous mutations in large populations. Genes that are particularly prone to be driven by positive selection include those involved with reproduction, immune response, sensory perception and apoptosis. Genetic innovations are also frequently obtained by the gain or loss of complete gene sequences. Moreover, it is increasingly realized, from comparative genomics, that purifying selection conserves much more than just the protein‐coding part of the genome, and this points at an important role for regulatory elements in trait evolution. Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution.
PROTEIN TURNOVER IN CELL‐ENRICHED FRACTIONS FROM RABBIT BRAIN 1

Abstract— A modification of the available methods was used for preparation of nerve and glia cell‐enriched fractions from rabbit brain and spinal cord. The rate of incorporation of tritiated leucine and the turnover rates of protein during 10 days was studied in the bulkprepared cell fractions. The rate of incorporation into the nerve cell fraction was approximately three times greater than in the glia fraction. The nerve cells had one rapid and one slow phase in decline of radioactivity, while the glial cells were characterized by a more uniform decline. The soluble radioactivity was followed in whole tissue of brain and spinal cord and certain differences between the two were observed.
Footwear and Balance in Older Men

To the Editor-At the annual meeting of the South Dakota State Medical Association, I was rendered speechless by a proposed resolution "that the American Medical Association seek to have funding of long-term care removed from the health care calculations, and that Medicaid funds not be mandated to be expended on long-term care, and that federal and state officials directly address long-term care and other social needs of the elderly through separate social legislation regarding budget, financing, and administration. " Taken by surprise, I was unable to articulate my disagreement to this proposal at our House of Delegates meeting. In retrospect, I should have pointed out that the only motivation for such a proposal must be to decrease significantly the calculation of our nation's total health care bill, thereby diminishing the perception that health care is too expensive and, in turn, maintaining the status quo. I would have pointed out that the drawback to this policy is that it will further separate long-term-care geriatrics from mainstream medicine and discourage efforts to increase remuneration equitably for physicians' services in long-term care. I should have espoused the position that the social needs of elders in long-term care are inseparable from their medical needs. I should also have said that the intensity of medical care and rehabilitative services in our nation's nursing homes has dramatically increased, especially since DRG's came into effect, causing many elders to make recuperative stays in nursing facilities after discharge from the acute care hospital. Nursing homes are no longer primarily domiciliary. Our patients are increasingly complex and run the gamut from very high rehabilitation potential to hospice. I was saddened to see that the Interim Business Meeting of the AMA in Nashville this December overwhelmingly advocated this policy.
A defected core highly birefringent dispersion compensating photonic crystal fiber

In this paper we propose a defected core Photonic Crystal Fiber (PCF) having circular lattice that ensures Residual Dispersion Slope (RDS) matched negative dispersion covering S+C+L communication bands with high birefringence for sensing purpose. The results show that this PCF has an average value of negative dispersion of -331 ps/nm-km & offers high birefringence of 2.75×10-2 with relative dispersion slope (RDS) perfectly matched to that of single mode fiber of about 0.0036 nm-1 at the wavelength 1550 nm. Due to its optical properties, the proposed fiber can be considered as an excellent candidate for sensing applications by maintaining single polarization along with dispersion compensation in optical fiber transmission system.
Violence among Street-Involved Youth: The Role of Methamphetamine

Aims: This study investigated a possible association between violence and the use of drugs, particularly methamphetamine and alcohol. Methods: Cross-sectional, baseline data were derived from the At-Risk Youth Study, a prospective cohort of street-involved youth in Vancouver, Canada. Subjects were asked whether they had suffered or perpetrated violence in the 6 months prior to the interview. Results: In total, 478 youth were enrolled, with a median age of 22 years (interquartile range = 20.0–23.9); 230 (48%) reported having been victims of violence, while 165 (34.5%) reported having perpetrated violence. Daily methamphetamine use was not associated with either outcome. In a multivariate analysis, daily alcohol consumption was significantly associated with being a victim (adjusted odds ratio = 2.10) and a perpetrator (adjusted odds ratio = 2.02) of violence. A history of abuse, failing a grade, and dealing drugs were also independently associated with violence, while having a regular partner was protective. Conclusion: Contrary to popular media reports that methamphetamine causes violence, we found no association. The association of alcohol with violence, though, has implications for screening and intervention programs.
Automatic polarization-mode dispersion compensation in 40-Gbit/s transmission

We believe we demonstrated automatic polarization-mode dispersion (PMD) compensation in 40-Gbit/s NRZ transmission for the first time. By the feedback control of an optical PMD compensator to maximize the 20-GHz intensity of received baseband signals, we more than doubled the allowable PMD from 11 to 23 ps.
A simple and effective method for microstrip dual-band filters design

A new type of novel low loss dual-band microstrip filters using folded open-loop ring resonators (OLRRs) is presented in this letter. Both magnetic and electric coupling structures are implemented to provide high performance passband response. The first passband and second passband of the designed dual-band filter can be easily and accurately shifted to a desired frequency band by adjusting the physical dimensions of OLRRs. Finally, the 2.4-GHz/5.7-GHz and 2.4-GHz/5.2-GHz dual-band filters are illustrated and measured in this letter.
Blutdruckvariabilität

Die permanenten Fluktuationen des Blutdrucks sind für den Patienten immer wieder überraschend („Herr Doktor, mein Blutdruck schwankt so.“); sie haben aber auch große klinische Bedeutung. Das Ausmaß der hypertensiven Organschäden wird nicht nur von der absoluten Blutdruckhöhe bestimmt, sondern auch von der Variabilität des Blutdrucks. Blutdruckvariabilität ist ein (unabhängiger) Prädiktor für kardiovaskuläre Ereignisse [6, 11, 14, 25, 28, 30, 31, 33]. Sie umfasst die Schwankungen mit jeder Herzaktion (beatto-beat), Tag-Nacht-Schwankungen, Schwankungen von Tag zu Tag und saisonale Variationen. Eine erhöhte Blutdruckvariabilität am Tage erhöht das Risiko, während eine normale nächtliche Blutdruck-Senkung das Risiko vermindert. Die Blutdruckvariabilität ist bei Hypertonikern ausgeprägter und frequenter als bei Normotonikern und nimmt mit dem Alter zu.
Evaluation of liver metastases after radiofrequency ablation: utility of 18F-FDG PET and PET/CT.

OBJECTIVE Our objective was to review the CT appearance of liver metastases after radiofrequency ablation and to describe the imaging findings of and utility of (18)F-FDG PET and PET/CT in assessing tumor recurrence after ablation. CONCLUSION (18)F-FDG PET and PET/CT can provide added diagnostic information compared with conventional imaging in patients after radiofrequency ablation of liver metastases and can be useful in guiding repeat ablation procedures.
Information Technology and Quantitative Management ( ITQM 2013 ) Advertisement Click-Through Rate Prediction using Multiple Criteria Linear Programming Regression Model

In advertisement industry, it is important to predict potentially profitable users who will click target ads (i.e., Behavioral Targeting). The task selects the potential users that are likely to click the ads by analyzing user's clicking/web browsing information and displaying the most relevant ads to them. In this paper, we present a Multiple Criteria Linear Programming Regression (MCLPR) prediction model as the solution. The experiment datasets are provided by a leading Internet company in China, and can be downloaded from track2 of the KDD Cup 2012 datasets. In this paper, Support Vector Regression (SVR) and Logistic Regression (LR) are used as two benchmark models for comparison. The results indicate that MCLPR is a promising model in behavioral targeting tasks.
My dear robot : anthropomorphism and loneliness

Over the last years a more refined picture over the concept of anthropomorphism develop. Where before the focus lay primarily on the questions of where and to what extend anthropomorphism occurs, now a theory on the how emerged. The Three-Factor theory (Epley, Waytz, & Cacioppo, 2007) gives an underlying mechanism that could explain how anthropomorphism forms. In the context of the more and more relevant topic of human-robot interaction this study tries to shed more light onto how sociality motivation influences the anthropomorphisation of robots. To answer this research questions it was tested if chronic loneliness and/or situational loneliness positively influence the anthropomorphisation of robots. Al 27 respondents had to rate 20 videos of different robots on a ‘Perceived Humanness’. To assess the dispositional loneliness they were asked to fill out the ‘UCLA Loneliness’ scale. For the situational loneliness an experimental condition was implemented. The results were analysed through a correlation analysis and a Linear Mixed Model regression. The results of this research could only partly support previous findings and the Three-Factor theory, as only the situational factor revealed a significant influence on the anthropomorpisation of robots. More research is needed to further confirm and evaluate this findings.
Frequency-Domain Packet Scheduling for Low PAPR in 3GPP LTE Uplink

Single carrier frequency domain multiple access (SC-FDMA) has been adopted for the 3GPP long-term evolution (LTE) uplink multiple access scheme due to the power consumption issue of mobile handsets. Like OFDMA in the downlink, SC-FDMA enables multiple users to be served simultaneously in the uplink. However, all subcarriers allocated to a single user must be contiguous in the frequency domain at each time slot due to its single carrier property. This contiguous allocation constraint makes scheduling difficult. A scheduling scheme in such systems needs to keep this constraint whilst trying to satisfy its own objectives. Therefore, we propose a frequency-domain packet scheduling algorithm to lower the PAPR of the mobile handset under this constraint. In this paper, we perform system level simulation on the 3GPP LTE system model. We compare the proposed scheme and previous one in terms of system throughput, fairness, and PAPR.
Detecting Overlapping Community Structures with PCA Technology and Member Index

The community structures reflect the basic property of social networks. How to effectively detect them is difficult and important. Traditional solutions such as nonnegative matrix factorization approaches have a high time and space complexity, resulting in a poor scalability. In this paper, we propose PCA-MI, a novel method to detect the overlapping community structures. Firstly, we use the principle component analysis (PCA) technology to extract key features of network information, and then employ membership index (MI) to classify nodes. Experimental results show that our approach can fast identify the overlapping community structures and achieve approximate Module-Q values as the traditional algorithms.
Pipelined Adders

A well-known scheme for obtaining high throughput adders is a pipeline in which each stage contains an array of half-adders performing a carry-save addition. This paper shows that other schemes can be designed, based on the idea of pipelining a serial-input adder or a ripple-carry adder. Such schemes offer a considerable savings of components while preserving high throughput. These schemes can be generalized by using (p,q) parallel counters to obtain pipelined adders for more than two numbers.
On the Power of Planned Infections in Networks

Over the last decade we have witnessed the rapid proliferation of online networks and Internet activity. Although such activity is generally considered a blessing, it also brings with it a large increase in risk of computer malware—malignant software that actively spreads from one computer to another. To date, the majority of existing models of malware spread use stochastic behavior, when the set of neighbors infected from the current set of infected nodes is chosen obliviously. In this work, we initiate the study of planned-infection strategies that can decide intelligently which neighbors of infected nodes to infect next in order to maximize their spread, while maintaining a “signature” similar to the oblivious stochastic infection strategy in order not to be discovered. We first establish that computing optimal and near-optimal planned strategies is computationally hard. We then identify necessary and sufficient conditions in terms of network structure and edge infection probabilities such that the planned process can infect polynomially more nodes than the stochastic process while maintaining a similar “signature” as the oblivious stochastic infection strategy. Among our results is a surprising connection between an additional structural quantity of interest in a network, the network toughness, and planned infections. Based on the network toughness, we characterize networks where existence of planned strategies that are pandemic (infect all nodes) is guaranteed, as well as efficiently computable.
The recursive companion matrix root tracker

A new sequential O(n/sup 2/) polynomial factorization algorithm that updates all roots of an nth-order polynomial with real time-varying coefficients simultaneously and efficiently in response to coefficient perturbations is introduced. The algorithm is based on a variant of sequential orthogonal iteration and exploits the special structure of the coefficient companion matrix. All internal operations are based on real passive Givens plane rotations and real matrix-vector multiplications. The algorithm is unconditionally stable and requires no initial guess of the root values. Numerical examples are presented to demonstrate the performance of the algorithm. Comparisons are made to the Starer and Nehorai (1991) root tracking algorithm.
Environmental dissolved organic matter governs biofilm formation 1 and subsequent linuron-degrading activity of a linuron-degrading 2 bacterial consortium 3 Running title : Linuron degradation by DOM grown biofilms

Corresponding author: 11 Prof. dr. ir. Dirk Springael 12 Division of Soil and Water Management 13 Faculty of Bioscience Engineering, Catholic University of Leuven 14 Kasteelpark Arenberg 20 – bus 2459 15 B-3001 Heverlee 16 Belgium 17 Tel: ++3216321604 18 Fax: ++3216321997 19 e-mail: dirk.springael@ees.kuleuven. be 20 keywords: consortium/ biofilm / dissolved organic matter / linuron biodegradation / 21 synergy 22
Crystal structure of an archaeal specific DNA‐binding protein (Ape10b2) from Aeropyrum pernix K1

DNA binding proteins are essential in all organisms, and they play important roles in both compacting and regulating the genetic material. All thermophilic and hyperthermophilic archaea encode one or more copies of Alba or Sso10b, which is a small, abundant, basic protein that binds DNA. Here, we present the crystal structure of Ape10b2 from Aeropyrum pernix K1 at 1.70 Å. Although the overall structure resembles the known Alba protein fold, a significant conformational change was observed in the loop regions. Specifically, the L5 loop is slightly longer, as compared to those of other known proteins, and the flexibility of this loop may facilitate the interaction with double stranded DNA. In addition, we showed that Ape10b2 binds to 16 and 39 bp duplex DNAs with high affinity. On the basis of our analyses, we have created a putative protein‐DNA complex model. Proteins 2008. © 2007 Wiley‐Liss, Inc.
A systematic review of interactive information retrieval evaluation studies, 1967-2006

With the increasing number and diversity of search tools available, interest in the evaluation of search systems, particularly from a user perspective, has grown among researchers. More researchers are designing and evaluating interactive information retrieval (IIR) systems and beginning to innovate in evaluation methods. Maturation of a research specialty relies on the ability to replicate research, provide standards for measurement and analysis, and understand past endeavors. To this end, this article presents a historical overview of 40 years of IIR evaluation studies using the method of systematic review. Two thousand, seven hundred and ninety-one journal and conference units were manually examined and 127 articles were selected for analysis in this study based on pre-defined inclusion and exclusion criteria. These articles were systematically coded using features such as author, publication date, source and references and properties of the research method used in the articles such as number of subjects, tasks, corpora and measures. Results include data describing the growth of IIR studies over time, the most frequently occurring and cited authors and sources, and the most common types of corpora and measures used. An additional product of this research is a bibliography of IIR evaluation research which can be used by students, teachers and those new to the area. To the authors’ knowledge, this is the first historical, systematic characterization of the IIR evaluation literature, including the documentation of methods and measures used by researchers in this specialty.
A 0.8 V/100 MHz/sub-5 mW-operated mega-bit SRAM cell architecture with charge-recycle offset-source driving (OSD) scheme

A 0.8 V/100 MHz/sub-5 mW-operated 1-Mbit SRAM cell architecture which uses a charge-recycle offset-source driving (OSD) scheme, is proposed. This paper is focused on why OSD can reduce the power dissipation to /spl les/1/14 compared to the previously reported negative source drive (NSD) scheme, while achieving a 0.8 V/100 MHz operation. OSD features as follows: (1) "parallel shift" of the potential of storage-node pairs V/sub H//V/sub L/ (0.8 V/0 V->1.4 V/0.6 V) for the unselected cell, (2) source line over-drive (0.6 V->0 V) when accessing the cell, (3) column-decoded source line drive in wordline (WL) direction, enabling to realize a pseudo cross-point access, and (4) charge-recycling source line drive, making it possible to eliminate the power-loss when resetting the potential of source line (0 V->0.6 V). OSD no longer requires negative-bias (-0.6 V) pumping circuit which has an intolerable-low supply-efficiency at 0.8 V Vcc, necessary to realize the source over-driving, unlike NSD. Thus, OSD can be exploited to realize 75% over-driving of source line (V/sub Gs/=0.8 V->1.4 V) necessary to achieve 100 MHz-operation, without an intolerable power-loss, instead of NSD. To demonstrate the effectiveness of OSD, power consumption comparisons were made between this work and NSD. For all measurements, the same access time conditions were used based on the simulated and measured data of the 0.35 /spl mu/m 1 Mbit-CMOS SRAM (16 K-word/spl times/64-bit). OSD enables a dramatic power reduction of over 93%, while maintaining 100 MHz operation even at 0.8 V Vcc, compared to NSD.
Die Bedeutung der Sonografie bei der Abklärung von Schilddrüsenerkrankungen

Zusammenfassung Schilddrüsenknoten und Schilddrüsenveränderungen sind häufige Befunde in der Allgemeinbevölkerung. Die Sonografie ist dabei das wichtigste bildgebende Instrument der Schilddrüsendiagnostik. In Zusammenschau des sonografischen Befunds mit basalen Schilddrüsenhormonparametern und dem klinischen Bild lässt sich in der überwiegenden Zahl der Fälle bereits eine korrekte Diagnose stellen – wie z. B. Hashimoto-Thyreoiditis, eine diffuse Struma oder ein Morbus Basedow – und eine entsprechende Therapie einleiten. Eine sichere Unterscheidung hormonaktiver und inaktiver Knoten sowie insbesondere benigner und maligner Knoten ist jedoch sonografisch nicht sicher möglich. In der Diffenzialdiagnose der Hormonaktivität von Schilddrüsenknoten hat die Szintigrafie ihre klinische Bedeutung. Zur Risikostratifizierung des Malignitätsrisikos von Knoten wurde in den vergangenen Jahren versucht, durch standardisierte Befunderhebung evaluierter Risikofaktoren eine bessere Selektion von Patienten, die einer weiteren Diagnostik zugeführt werden sollen, zu erzielen. Entsprechend des „Breast Imaging Reporting and Data System“ (BI-RADS), das standardisierte Malignitäts- bzw. Benignitätskategorien mit evaluierten prozentualen Malignitätswahrscheinlichkeiten als Grundlage für das weitere klinische Management definiert, wurde analog ein „Thyroid Imaging Reporting and Data System“ (TI-RADS) vorgeschlagen. Neuere technische Verfahren, wie die Elastografie, zeigen ebenfalls vielversprechende Daten und könnten Eingang in den klinischen Alltag gewinnen. Die sonografisch gesteuerte Feinnadelpunktion ist das zentrale Element in der Diagnostik sonografisch suspekter Schilddrüsenknoten und trägt wesentlich zur Sicherung der Diagnose Malignität vs. Benignität bei.