Miracle-dz/UniFAR-FTUs huggingface dataset:
Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush-tailed rock-wallaby (Petrogale penicillata;n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush-tailed rock-wallabies, whose divergence appears to date to the mid-Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north–south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush-tailed rock-wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.
IN VITRO MUTAGENESIS IN BANANA AND VARIANT SCREENING THROUGH ISSR

An efficient culture medium for In vitro clonal propagation of banana cultivars was established. Meristamtic tips of Basrai and GCTCV-215 were irradiated with different doses of gamma rays viz., 0, 10, 20, 30 and 40Gy through cobalt 60 source. Eleven random ISSR primers were used to study genetic variation among the radiated population. ISSR primers produced 37 bands in all the clones studied. Two monomorphic and 35 polymorphic bands were observed during the study. The number of fragments produced by the primers ranged from 2-5, with an average of 3.45 fragments. Fragments size ranged from 198bp-1.842kb. Genetically most similar genotypes were G-215MP3 and G-215MP4 (89.8%) while most dissimilar genotypes were Basrai and G-215MP2 (38.5%). On the basis of similarity matrix clones could be divided into three clusters and two groups.
Disturbance attenuation type distributed control for identical decoupled linear systems

We propose a design method of disturbance attenuation type distributed control for identical decoupled linear systems together with conditions for stability of the closed loop global system. Using a simple example of formation flight corrupted by disturbances, we compare the design by the proposed method with that by the LQ control method in Borrelli and Keviczky (2006); we consider two kinds of disturbances, system disturbances and parameter variation. And we demonstrate that proposed method has superior robustness against disturbances.
Term Weighting Schemes for Question Categorization

Term weighting has proven to be an effective way to improve the performance of text categorization. Very recently, with the development of user-interactive question answering or community question answering, there has emerged a need to accurately categorize questions into predefined categories. However, as a question is usually a piece of short text, can the existing term-weighting methods perform consistently in question categorization as they do in text categorization? The answer is not clear, since to the best of our knowledge, we have not seen any work related to this problem despite of its significance. In this study, we investigate the popular unsupervised and supervised term-weighting methods for question categorization. At the same time, we propose three new supervised term-weighting methods, namely, gf* icf, igf* gf* icf, and vrf. Comparisons of them with existing unsupervised and supervised term weighting methods are made through a series of experiments on question collections of Yahoo! Answers. The experimental results show that igf* gf* icf achieves the best performance among all term-weighting methods, while gf*icf and vrf are also competitive for question categorization. Meanwhile, tf* OR is proven to be the most significant one among existing methods. In addition, igf* gf* icf and vrf are also effective for long document categorization.
A novel evolutionary engineering design approach for mixed-domain systems

This paper presents an approach to engineering design of mixed-domain dynamic systems. The approach aims at system-level design and has two key features: first, it generates engineering designs that satisfy predefined specifications in an automatic manner; second, it can design systems belonging to different or mixed physical domains, such as electrical, mechanical, hydraulic, pneumatic, thermal systems and/or a mixture of them. Two important tools are used in this approach, namely, bond graphs and genetic programming. Bond graphs are useful because they are domain independent, amenable to free structural composition, and are efficient for classification and analysis, allowing rapid determination of various types of acceptability or feasibility of candidate designs. Genetic programming, on the other hand, is a powerful tool for open-ended topological search. To prevent the premature convergence often encountered in evolutionary computation, a hierarchical fair competition model is adopted in this work. Examples of an analog filter design and an MEM filter design illustrate the application of the approach.
A Health-Related Quality-of-Life Measure for Use in Patients with HIV: A Validation Study

&NA; In the United States, HIV has evolved from an acute disease to a chronic illness making health‐related quality of life a pre‐eminent goal for many persons living with HIV (PLWH). There have been a number of HIV‐specific quality‐of‐life instruments developed, but little attention has been paid to the validation of standardized nondisease‐specific quality‐of‐life instruments tailored to PLWH. The goal of this research was to validate the Patient‐Reported Outcomes Measurement Information System (PROMIS)‐29, a questionnaire that measures health‐related quality of life in PLWH. A sample of 1306 PLWH completed an online anonymous survey assessing their symptom experience and health‐related quality of life. A subsample of 209 participants completed another questionnaire 30 days later. The subscales of the PROMIS‐29 showed high internal consistency reliability (range = 0.87–0.97). The PROMIS‐29 detected differences in health‐related quality of life in those persons who reported an AIDS diagnosis compared to those who did not report an AIDS diagnosis. The PROMIS‐29 has demonstrated reliability, validity, and reproducibility for use in measuring health‐related quality of life in PLWH.
De novo detection and accurate False Discovery Rate control of differentially methylated regions from Whole Genome Bisulfite Sequencing : Supplementary Materials

The SRA Toolkit (SRA) was used to download all SRA files listed at the accession numbers SRP000941 (UCSD Human Reference Epigenome Mapping Project), SRP074072 (Yang, et al., 2016). These two studies contained single end and paired end reads, respectively. Fastqc (Andrews, 2010) was used to extract fastq files and evaluate base quality scores. Trim Galore version 0.4. 1 (Krueger, 2015) was used to remove base calls with a Phred score of 20 or lower, remove adapter sequences, and remove sequence pairs where a read became too short as a result of trimming (less than 20 base pairs) while keeping sequence pairs in sync. Bismark (Krueger and Andrews, 2011) version 0.16. 3_dev obtained from GitHub (https://github.com/FelixKrueger/Bismark) was used to align and map the trimmed fastq files using the Botwie2 option and the GRCh38 version of the human genome (from the assembly file: ftp.ensembl.org/pub/release84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna. primary_assembly.fa.gz, downloaded on July 26, 2016) and the GRCm38 version of the mouse genome (from the assembly file: ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/ Mus_musculus.GRCm38.dna.primary_assembly.fa.gz, downloaded on 24 June 2016). Samtools (Li, et al., 2009) was used to combine the resulting bam files for samples that were split into multiple runs. The bismark_methylation_extractor command within Bismark was used to obtain the count of reads corresponding to methylation and no methylation at each CpG site that had coverage in the genome. Post-mapping deduplication of reads was not performed since the datasets had widely varying coverage levels and this practice is not generally advisable on lowcoverage samples.
The influence of quantum-well composition on the performance of quantum dot lasers using InAs-InGaAs dots-in-a-well (DWELL) structures

The optical performance of quantum dot lasers with different dots-in-a-well (DWELL) structures is studied as a function of the well number and the indium composition in the InGaAs quantum well (QW) surrounding the dots. While keeping the InAs quantum dot density nearly constant, the internal quantum efficiency /spl eta//sub i/, modal gain, and characteristic temperature of 1-DWELL and 3-DWELL lasers with QW indium compositions from 10 to 20% are analyzed. Comparisons between the DWELL lasers and a conventional In/sub 0.15/Ga/sub 0.85/As strained QW laser are also made. A threshold current density as low as 16 A/cm/sup 2/ is achieved in a 1-DWELL laser, whereas the QW device has a threshold 7.5 times larger. It is found that /spl eta//sub i/ and the modal gain of the DWELL structure are significantly influenced by the quantum-well depth and the number of DWELL layers. The characteristic temperature T/sub 0/ and the maximum modal gain of the ground-state of the DWELL structure are found to improve with increasing indium in the QW It is inferred from the results that the QW around the dots is necessary to improve the DWELL laser's /spl eta//sub i/ for the dot densities studied.
University ’ s repository of research publications and other research outputs Anti-MUC 1 aptamers : radiolabelling with 99 m Tc and biodistribution in MCF-7 tumour-bearing mice

Introduction: Aptamers previously selected against the protein core (AptA) or the tumour glycosylated (AptB) MUC1 glycoprotein have been conjugated to MAG2 and labelled with Tc, for the potential use as radiopharmaceuticals for diagnostic imaging of breast cancer. Methods: The conjugation was achieved in high yield using standard peptide coupling reactions between an amino modification on the aptamer and the activated carboxylic group on the ligands. The retention of the affinity of the MAG2 modified AptA for the MUC1 protein core was confirmed using a FID binding assay. The
Inaccuracies in Network Realization of Rational Models Due to Finite Precision of RLC Branches

One of the most challenging points in the simulation of power system transients is the modeling of frequency dependent impedances or admittances and their inclusion in the simulation environment. Highly accurate models can be identified via rational function approximations in the frequency domain, for instance by Vector Fitting. One way of including the obtained model in a time domain simulation is via an equivalent electrical circuit. This paper shows a case where the modeling via an equivalent circuit in ATP gives an inaccurate representation of the rational model. It is shown that the finite precision of the branch cards causes a catastrophic cancellation error in the representation of an RLCG branch. The sensitivity to the output format is investigated.
CMOS APS imager employing 3.3 V 12 bit 6.3 MS/s pipelined ADC

A novel 256/spl times/256 CMOS active pixel sensor (APS) system with 12 bit, 6.3 Msample/s (MS/s) CMOS pipelined analog to digital converter (ADC) integrated on chip is presented. The test chip has been implemented in 0.35 /spl mu/m 2P4M process, operated by a 3.3 V supply and is expected to dissipate 55 mW. The total area of the prototype is 12 mm/sup 2/, and the core area of ADC is 18% from the total area. System architecture and operation are discussed and simulation results are presented.
Recycling of particle- and fibreboards using the extruder technique

The wood composite industry is mainly a world-wide creation of the last century. The pace of development has been rapid and a continued high speed development is also expected for this century. Technological breakthroughs with new processing machines, quality control devices, better adhesives and use of other lignocellulosics than wood as a raw material will possibly play a great role in the future of this industry.
Synlet: an R package for systemically analyzing synthetic lethal RNA interference screen data

Summary High-throughput synthetic lethal RNA interference (RNAi) screen experiments shed important insights on the filed of cancer researches and drug discovery, but a comprehensive software for analyzing the data was not available yet. We present synlet, an R package provided a complete pipeline to process the synthetic lethal RNAi screens data. Synlet provides several methods to access the screen quality, including Z’ factor and data visualization. B-score and fraction of control or samples normalization methods are implemented in the package. More importantly, synlet facilitates the process of hits selection by implementing several algorithms, providing the possibility to identify high confidence targets. Availability The source code is freely available in Bioconductor (http://bioconductor.org/). Contact c.shao@Dkfz-Heidelberg.de
Adult age differences in episodic memory: further support for an associative-deficit hypothesis.

This study further tested an associative-deficit hypothesis (ADH; M. Naveh-Benjamin, 2000), which attributes a substantial part of older adults' deficient episodic memory performance to their difficulty in merging unrelated attributes-units of an episode into a cohesive unit. First, the results of 2 experiments replicate those observed by M. Naveh-Benjamin (2000) showing that older adults are particularly deficient in memory tests requiring associations. Second, the results extend the type of stimuli (pictures) under which older adults show this associative deficit. Third, the results support an ADH in that older adults show less of an associative deficit when the components of the episodes used are already connected in memory, thereby facilitating their encoding and retrieval. Finally, a group of younger adults who encoded the information under divided-attention conditions did not show this associative deficit.
Large-scale Models Reveal the Two-component Mechanics of Striated Muscle

This paper provides a comprehensive explanation of striated muscle mechanics and contraction on the basis of filament rotations. Helical proteins, particularly the coiled-coils of tropomyosin, myosin and α-actinin, shorten their H-bonds cooperatively and produce torque and filament rotations when the Coulombic net-charge repulsion of their highly charged side-chains is diminished by interaction with ions. The classical “two-component model” of active muscle differentiated a “contractile component” which stretches the “series elastic component” during force production. The contractile components are the helically shaped thin filaments of muscle that shorten the sarcomeres by clockwise drilling into the myosin cross-bridges with torque decrease (= force-deficit). Muscle stretch means drawing out the thin filament helices off the cross-bridges under passive counterclockwise rotation with torque increase (= stretch activation). Since each thin filament is anchored by four elastic α-actinin Z-filaments (provided with force-regulating sites for Ca2+ binding), the thin filament rotations change the torsional twist of the four Z-filaments as the “series elastic components”. Large scale models simulate the changes of structure and force in the Z-band by the different Z-filament twisting stages A, B, C, D, E, F and G. Stage D corresponds to the isometric state. The basic phenomena of muscle physiology, i. e. latency relaxation, Fenn-effect, the force-velocity relation, the length-tension relation, unexplained energy, shortening heat, the Huxley-Simmons phases, etc. are explained and interpreted with the help of the model experiments.
IL-6 gene amplification and expression in human glioblastomas

The aggressiveness of human gliomas appears to be correlated with the upregulation of interleukin 6 (IL-6) gene. Using quantitative PCR methods, we detected amplification and expression of the IL-6 gene in 5 of 5 primary glioblastoma samples and in 4 of 5 glioblastoma cell lines. This finding suggests that the amplification of IL-6 gene may be a common feature in glioblastomas and may contribute to the IL-6 over-expression. © 2001 Cancer Research Campaign http://www.bjcancer. com
Nurses’ Cyberloafing and Its Relationship to Procrastination and Conscientiousness in Damanhour National Medical Institute

Cyber-loafing involves an unproductive use of time in the workplace and distracts employees from their responsibilities and duties. This study was conducted because there is a risk posed on patient's safety if nurses are cyberloafing and if this behavior has a direct relation with procrastination and lack of conscientiousness. Aim of the study: to determine the relationship between cyberloafing, procrastination and conscientiousness among staff nurses working in Damanhour National Medical Institute. Research Design: A cross-sectional descriptive correlational design with a self-reporting questionnaire was used to obtain data. Setting: The study was conducted in all inpatients units except Intensive Care Units (N=10) in Damanhour National Medical Institute. Subjects: A convenience sampling technique was used to recruit the participants of 157 (professional and technical nurses) were present and agreed to participate in the study. Instruments: The questionnaire consisted of three main scales and a demographic data sheet. The scales were namely; cyberloafing scale, procrastination scale, and conscientiousness scale. Results: There are significant correlations between cyberloafing variety and cyberloafing frequency, procrastination and conscientiousness where p= <0.001 for the three variables respectively. Regarding, cyberloafing frequency, a negative significant correlation was found with procrastination where p= <0.001 and a positive significant correlation with conscientiousness where p= 0.048. Another positive significant correlation was found between procrastination and conscientiousness in which p= <0.001. Recommendations: more extensive and in-depth research on procrastination and conscientiousness in a private sector, where there is more availability of personal computer and internet connections would be beneficial.
Teaching A-level in early career: induction, support and professional learning

There is considerable interest within mathematics teacher education in mapping the career development of teachers. Although there is agreement that professional learning is embedded in workplace practice, there has been little attention to the effect of variations within the teaching profile. This paper focuses on pre-university mathematics and its contribution to teacher development in the early career stage. Our longitudinal multiple-case study mapped induction for A-level teaching in England, and identified opportunities and demands that led to professional learning. We found a common understanding of such teaching as a privilege. Teachers experienced rapidly reducing formal support, with little mentoring directed at reflective development of A-level teaching, and claimed this limited their growth as teachers. However, A-level teaching offered professional learning opportunities complementary to those offered by teaching of earlier mathematics: teachers came to better appreciate connections within mathematics, and the need for development of rigour and deep conceptual foundations, as well as deepening their own mathematical knowledge.
Arabic Short Answer Scoring with Effective Feedback for Students

In this paper, we explore text similarity techniques for the task of automatic short answer scoring in Arabic language. We compare a number of string-based and corpus-based similarity measures, evaluate the effect of combining these measures, handle student’s answers holistically and partially, provide immediate useful feedback to student and also introduce a new benchmark Arabic data set that contains 50 questions and 600 student answers. Overall, the obtained correlation and error rate results prove that the presented system performs well enough for deployment in a real scoring environment. General Terms Natural Language Processing, Text Mining
A Scalable Framework for CSI Feedback in FDD Massive MIMO via DL Path Aligning

Unlike the time-division duplexing systems, the downlink (DL) and uplink (UL) channels are not reciprocal in the case of frequency-division duplexing (FDD). However, some long-term parameters, e.g., the time delays and angles of arrival of the channel paths, enjoy reciprocity. In this paper, by efficiently exploiting the aforementioned limited reciprocity, we address the DL channel state information (CSI) feedback in a practical wideband massive multiple-input multiple-output system operating in the FDD mode. With orthogonal frequency-division multiplexing waveform and assuming frequency-selective fading channels, we propose a scalable framework for the DL pilots design, DL CSI acquisition, and the corresponding CSI feedback in the UL. In particular, the base station (BS) can transmit the FFT-based pilots with carefully selected phase shifts. Then, the user can rely on the so-called time-domain aggregate channel to derive the feedback of reduced dimensionality according to either its own knowledge about the statistics of the DL channels or the instruction from the serving BS. We demonstrate that each user can just feed back one scalar number per DL channel path for the BS to recover the DL CSIs. Comprehensive numerical results further corroborate our designs.
The Younger the Better ? Variability in Language Development of Young German-speaking Children with Cochlear Implants

The influence of age at implantation and experiential factors on language development in young children with cochlear implants was examined. There were two samples, one cross-sectional with 41 children, and one longitudinal with 26 children. Age at implantation in both samples ranged from 6 to 47 months, with children evenly distributed in the age groups: 6-12, 13-24, 25-42 months at implantation. Linguistic progress was assessed by parental questionnaire, and for the longitudinal sample additionally, by one-hourly spontaneous speech samples. Data were collected 12, 18, 24 and 30 months after implantation. Measures of vocabulary and grammar were taken, including number of word types, MLU, inflectional morphology and sentence complexity. In both samples there was extensive variability in linguistic progress. Children’s linguistic progress was significantly related to social class, measured by parental education, but not age at implantation. Maternal dialogue variables were analyzed in the longitudinal sample and found to be related to children’s linguistic progress. Thus, experiential factors account for the extensive variability in children’s linguistic growth rather than age at implantation. The data support an epigenetic rather than a maturational concept of ‘sensitive phase’.