Miracle-dz/UniFAR-FTUs huggingface dataset:
Methods to improve short fragment NGS analysis - with a focus on ancient DNA

The introduction of next-generation sequencing technologies led to an increase in the amount of sequencing data that needs to be analyzed. However, not all sequencing data are equally analyzable owing, for example, to differences in read length. This thesis addresses some of the problems related to the short reads generated by next-generation sequencing technologies. This is of great relevance, as most recent and ongoing sequencing projects still use next-generation sequencing. Admittedly, third generation sequencing, which is still in its infancy to date, promises the generation of much longer reads. However, some research questions cannot make use of these long-read technologies. A prominent example are ancient DNA projects that sequence fragments of DNA from ancient samples, which have degraded over time and are typically very short. The present thesis introduces several methods and programs addressing different research applications of next-generation sequencing data, which can be used especially when, as in the case of research on ancient DNA, have to deal with short fragments. We present methods for the reconstruction of the sequence of repetitive regions using only short reads by reconstructing each repetitive region separately, thus eliminating the problem of reads that map to multiple locations. Additionally, we present a two-layer approach to address the de novo assembly of short fragments, which generally contains reads of different lengths. Furthermore, we present an automated method to compare mapping-based reconstructions that share the same reference by analyzing them simultaneously. Finally, we present SNPViz, which visualizes amino acid affected by a SNP within the protein sequence and its corresponding three-dimensional structure. Taken together, this thesis presents several methods to improve the analysis of next-generation sequencing technologies. These methods can support researchers in better understanding their data and can help them uncover new foci for future research.
Document Title: A Model of Static and Dynamic Sex Offender Risk Assessment

The purpose of the present study was to test models of combining static and dynamic risk measures that might predict sexual recidivism among adult male sex offenders better than any one type of measure alone. Study participants were 759 adult male sex offenders under correctional supervision in Vermont who were enrolled in community sex offender treatment between 2001 and 2007. These offenders were assessed once using static measures (Static-99R, Static-2002R and VASOR) based on participants’ history at the date of placement in the community. A 22-item dynamic risk measure (SOTNPS) was used multiple times to assess participants, shortly after their entry into community treatment and approximately every six months thereafter. Analyses of SOTNPS scores resulted in the development of a new 16-item dynamic risk measure, the Sex Offender Treatment Intervention and Progress Scale (SOTIPS). At fixed oneand three-year follow-up periods from participants’ initial, second, and third dynamic risk assessments, the SOTIPS and Static-99R, the static risk measure selected for further analysis in the present study, each independently showed moderate ability to rank order risk for sexual, violent, and any criminal recidivism and return to prison. A logistic regression model that combined SOTIPS and Static-99R consistently predicted recidivism and outperformed either instrument alone when both instruments had similar predictive power. Participants who demonstrated treatment progress, as reflected by reductions in SOTIPS scores, showed lower rates of recidivism than those who did not.
Exploring logical connectors in journals with different indexing levels: A comparison between international and national indexed journals

Research to date has witnessed the mounting significance of logical connectors in writing including scientific journal articles; however, little is known as to whether the usage of such connectors may correspond to a varying degree of journal quality. This qualitative study fills in the void by exploring the use of logical connectors in journals with different indexing levels, national and international. Sixty articles were collected from two journals, thirty articles from each. Implicit behind this study is an assumption that differing journal indexing entails differing journal quality. Nineteen connectors that belong to the most frequently used conjunctive adverbials in academic prose were searched using Laurence Anthony’s concordance program (AntConc). The findings reveal that the top-two most frequently CAs used in both corpora are adversative however and causal therefore. Based on these results, the analysis is centered on these two CAs by investigating the coherence relations in order to see the underlying logical relationships between two sentences. The findings show that the illogical uses of CA however and therefore were equally found in both corpora although the percentages for the illogical use in the international journal articles are less than those in the national ones. In conclusion, not only do articles in the two journals share the same tendencies in the logical use, they also evince the same patterns of problem, namely failure in recognizing logical relationships and overuse of connectors. Of importance is that the purported relationship between journal indexation and logical use of connectors may be at best weak, and at worst absent, for both journals in question dominantly exhibit a logical usage of connectors. Pedagogical implications are also discussed.
Family of Nyquist-I Pulses to Enhance Orthogonal Frequency Division Multiplexing System Performance

ABSTRACT A family of Nyquist-I pulses called sinc parametric linear combination pulse (SPLCP) is proposed. It is characterized by two novel design parameters that provide additional degrees of freedom to minimize the intercarrier interference (ICI) power due to frequency offset. Moreover, it reduces the high peak-to-average power ratio (PAPR) value in orthogonal frequency division multiplexing (OFDM) systems. Several Nyquist-I pulses were recently proposed to address the subject of high sensitivity to frequency offset and high PAPR in OFDM-based transmissions. In this paper, we investigate the performance of SPLCP in terms of ICI power, signal-to-interference ratio (SIR) power, bit error rate (BER), and PAPR. We additionally examine the behaviour of SPLCP with new design parameters for a certain roll-off factor, α. We compare the performance of SPLCP with other well-known pulses. Theoretical and simulation results show that the proposed SPLCP outperforms other existing pulses in terms of ICI power, SIR power, BER, and PAPR.
Cut-offs and Gestures: Analytical Tools to Understand a Second Language Speaker

This paper will focus on one specific type of disfluency (speech less than fluent), that is, interruptions or cut-offs. The research on cut-offs has led to various hypotheses explaining how cut-offs are processed: Seyfeddinipur, Kita & Indefrey (2008) suggested that the cut-off is a controlled action and so on detecting the trouble the stop might be postponed, if necessary, to allow time for the resumption process; Tydgat, Stevens, Hartsuiker and Pickering (2011) added that the stopping and resumption processes are likely to occur concurrently and share the same resources. Therefore, the speaker has to decide whether it is more effective to stop and, if so, where. In Second Language Acquisition (SLA) error has been the topic of much discussion. However, disfluencies have surprisingly aroused less interest. SLA usually takes the view that any repair following a disfluency is the consequence of linguistic difficulties (usually grammar or vocabulary). However, like among native speakers, there are more reasons for disfluency and repair than just linguistic difficulties. A tool to aid disfluency analysis is that of the gesture performed together with speech. McNeill’s gesture theory holds that gesture and speech are two modalities of the same communicative process and that as such should be analysed together (2012). Therefore, the gesture might provide additional analytical information to the observer. investigate nature of cut-offs in using their also a second language. our the acquisition by our results native a Our results, based on a combination of qualitative and quantitative analysis, indicate that cut-offs, and the gestures associated with them, are used similarly by native speakers of both and the relationship between the cut-off and the or its the as well as providing evidence to support some of the existing hypotheses on cut-off production and gesture-speech relationships.
Analysis, Modeling, and Design of a 2.45-GHz RF Energy Harvester for SWIPT IoT Smart Sensors

Simultaneous wireless information and power transfer (SWIPT) is a flexible and cheap way to supply Internet-of-Things (IoT) smart sensors avoiding battery replacement. In this paper, we analyze, model, and design a 2.45-GHz RF energy harvesting (RFEH) system based on a discrete-component matching network (MN), a custom 65-nm CMOS cross-coupled rectifier, and an off-the-shelf storage-charging power management unit (PMU), which regulates the rectifier output voltage with maximum power point tracking (MPPT). We propose a reverse global analysis to model the RFEH. It allows an accurate prediction of the power harvesting efficiency (PHE) to directly size the MN and select the RFEH MPPT regulation ratio, at different incident RF power levels. We perform parasitic-aware RFEH design to take advantage of printed circuit board (PCB)/package capacitive parasitics at the rectifier input for optimizing the $\pi $ -MN with the help of the proposed RFEH modeling results. We show that this parasitic capacitance introduces a maximum bound on the real impedance at the rectifier input to ensure good impedance matching in practice. MPPT is used to help reach this target real impedance at given incident RF power, as the rectifier equivalent input impedance is a function of both its input and output voltages. Measurement results show a sensitivity as low as −17.1 dBm with a peak PHE of 48.3% at −3-dBm incident RF power. Global modeling, simulation, and measurement results demonstrate that the PHE is limited by PCB/package parasitic capacitance and that PCB/packaging technology improvement to reduce parasitic capacitance by 150 fF could boost the PHE up to 45% for a low incident RF power level of −10 dBm.
Back on the Street: Vienna, Copenhagen, Munich, and Rotterdam in focus

Abstract The paper presents a comparative study on neighbourhood streets in the densely populated cities of Rotterdam, Copenhagen, Munich, and Vienna. First, urban development is contextualized in a brief history of alternative street development approaches. Then, the current measures and strategies to transform streets into sufficient public spaces for a growing number of people are investigated. The analysis of street sections in the four cities revealed significant differences in the existing street layout but also similar planning strategies, a similar approach to the appropriation, and an aesthetics of informality in certain cases. Discussing the cities’ policies towards this reclamation, the paper shows how contemporary measures go beyond the simple recovery of traffic lanes for cyclists or creating pedestrian walkways. A conclusion is drawn that top-down building and design measures are merging with bottom-up or activated civic engagement and although the streets observed are in good condition, barrier-free, and well-maintained, improvements for streets as living environments are at an early stage.
Model Search for Statistical Machine Translation

Statistical machine translation builds complex probabilistic models from parallel corpora. As with any modelling task there is a trade-off between model accuracy and generalisation ability. This trade-off can be understood in terms of model complexity. The structure of translation models is typically chosen on the researchers intuitions, prejudices or interests. As such, these structures represent a manual sampling of the total space of possible translation models. There exist a number of methods to perform a more methodical form of model search in other domains of modelling. For example, the model merging algorithm of Stolcke and Omohundro (1992) is a method of searching the space of HMM models to find those with optimal complexity. A translation model merging algorithm is developed based on that algorithm. In experiment, its ability to find structures useful to the translation task is demonstrated and it is shown to outperform an appropriate baseline in translating from French to English.
Lung transplantation: improving clinical outcome and donor organ scarcity

Background Despite lung transplantation (LTx) being the golden standard for treating end-stage irreversible pulmonary disease, long-term outcome is yet to date significantly shorter when compared to survival of other solid organ Txs. Chronic lung allograft dysfunction (CLAD) and subsequently bronchiolitis obliterans syndrome (BOS) remains the major barrier to long-term success after LTx. The aim of this thesis was to identify predisposing factors / risk factors related to CLAD/BOS that influence pulmonary function and survival after lung transplantation. In addition to explore the hypothesis that different pulmonary graft preservation influence the outcomes in LTx. Methods This dissertation is based on the retrospective review of patient journals at Lund University Hospital from 19902016 and a porcine animal DCD lungtransplant model in the experimental aspect of this thesis. Results Overall 1-, 5-, 10-, 15and 20-year survival rates were 88, 65, 49, 37 and 19% for the whole cohort. Double-LTx (DLTx) had superior outcome compared with Single-LTx (SLTx) up to 20-year survival rates (p < 0.05). Cumulative incidence rates of BOS were 15% at 5 years, 26% at 10 years and 32% at 20 years. ABO-identical blood group matching showed no superior outcome to ABO-compatible matching (p > 0.05). In the experimental project, investigated blood gases in Donation after Circulatory Death (DCD) in addition to Ex Vivo Lung Perfusion (EVLP) using alteplase, all meet the criteria's for LTx, with no difference compared to the control group in macroscopic appearance (p > 0.05). Conclusion With a 25-year experience, excellent survival rates were shown giving our recipients one of the highest survival rates internationally. DLTx showed a superior survival capacity over SLTx, despite having a higher incidence of BOS. The present selection-bias of preferring ABO-identical lungs could be refined and help us implement more efficient organ allocation. Futhermore, DCD is a safe and effective method to expand the donor pool.
An Analysis of Fusion Center Collaboration in a Network Environment

In the aftermath of the terror attacks of September 11, 2001, the 9/11 Commission concluded that the nation’s Intelligence Community and the domestic counterterrorism model of information gathering and intelligence failed to “connect the dots. ” As a result the federal government initiated several new initiatives designed to break down the barriers and “silos” inhibiting information and intelligence sharing. One such initiative was the establishment of information sharing fusion centers. Fusion centers are state and local government operated information collection and analysis centers that serve state and local law enforcement with the prevention, detection, and deterrence of criminal and terrorism activity. Fusion centers are also part of a national network of fusion centers which provide important suspicious activity reports and other information to the federal government in support of the national counterterrorism mission. A key feature of fusion centers is the need to collaborate with state, local and federal public agencies and disciplines, and the private sector in order to collect information, process this information into useable and actionable intelligence, and disseminate this intelligence to customers, partners and stakeholders. Fusion centers are placed in a context of dealing with terrorism as a complex “wicked problem,” which generally requires using interorganizational collaboration and networks to successfully address such problems. This research analyzes how state and local fusion centers use collaboration to build and maintain information sharing networks supporting national, regional, and local area counterterrorism efforts.
Computerised analysis of fetal heart rate

This thesis presents a comprehensive work on computerised analysis of fetal heart rate (FHR) features, including feature extraction, feature selection, analysis of influencing factors and setting up/validation of a computerised decision support system. Firstly, a novel feature – pattern readjustment – was extracted and tested. Clinical data were used to train a Support Vector Machine (SVM) to detect pattern readjustment. Then, the association of pattern readjustment and adverse labour outcome was investigated. The validation results with clinical experts show that the pattern readjustment can be accurately detected, while the study on labour outcome shows that the feature is related to fetal acidemia at birth. Secondly, Genetic Algorithms were employed as a feature selection method to select a best subset of FHR features and to use them to predict fetal acidemia with linear and nonlinear SVM. The diagnostic power of the classifier output using selected features was tested on the total set of 7,568 cases. As the classifier output increases, there is a consistent increase of the risk of fetal acidemia. Thirdly, an important influencing factor on FHR features - signal loss – was investigated. A bivariate model was built to estimate error based on signal loss. Validation results show that the bivariate model can accurately predict the error generated by signal loss. The influence of signal loss on labour outcome classification was also investigated. Finally, a computerised decision support system to estimate the risk of fetal acidemia was set up based on the above studies. The system was validated using new retrospective data. Validation results show that the system is capable of predicting adverse labour outcome and providing timely decision support. It is the first time an intrapartum computerised FHR decision support system has been built and validated on this size of dataset. With further improvements, such a system could be implemented clinically in the long term.
A Variational Pan-Sharpening With Local Gradient Constraints

Pan-sharpening aims at fusing spectral and spatial information, which are respectively contained in the multispectral (MS) image and panchromatic (PAN) image, to produce a high resolution multi-spectral (HRMS) image. In this paper, a new variational model based on a local gradient constraint for pan-sharpening is proposed. Different with previous methods that only use global constraints to preserve spatial information, we first consider gradient difference of PAN and HRMS images in different local patches and bands. Then a more accurate spatial preservation based on local gradient constraints is incorporated into the objective to fully utilize spatial information contained in the PAN image. The objective is formulated as a convex optimization problem which minimizes two leastsquares terms and thus very simple and easy to implement. A fast algorithm is also designed to improve efficiency. Experiments show that our method outperforms previous variational algorithms and achieves better generalization than recent deep learning methods.
Seed position and influences on Caesalpinia pulcherrima germination and reserve proteins

Caesalpinia pulcherrima has diverse uses in the world, including ornamental and landscape characteristics, but there is a great disparity of germination during the time of seedlings production, being this factor attributed to the position of the seeds in fruits. This study aimed to evaluate some germinative aspects and concentration of reserve proteins in C. pulcherrima seeds in the function of its position in fruits. The work was carried out in greenhouse, in a completely random experimental design, with five seed position in the pod, based on the distance from seed to the peduncle (P1 - distal, P2 - distal/median, P3 - median, P4 -proximal/ median, P5 - proximal). Eight replicates with eight seeds each, were sowed to germinate for 21 days in expanded polystyrene trays filled with substrate. The percentage, speed index, average germination time and 50% germination time of the plantlets were evaluated. The reserve proteins (albumin, globulin, prolamin and glutelin) contents were also determined. There was influence of the position of the seed in the fruit on germination and reserve proteins contents. The proximal/median position showed excellent results, having correlations of albumin, globulin and glutelin concentrations with some germinative parameters. Therefore, the use of proximal/median position of the seeds is recommended for C. pulcherrima propagation.
2.2-4.6-GHz Active Quasi-Circulator with > 24-dB Transmit-Receive Isolation

An active quasi-circulator (AQC) integrated circuit is designed and fabricated in a 0.18-[Formula: see text]m CMOS process. The proposed design is based on a parallel combination of a common-source (CS) stage and a combined common-drain (CD) and common-gate (CG) topology. Scattering matrix of the core AQC circuit is derived considering MOSFET’s secondary effects, particularly the body effect as well as output loading effects. Measurements of the quasi-circulator reveal an insertion loss of [Formula: see text] dB between transmitter-to-antenna ports ([Formula: see text]) and of [Formula: see text] dB between antenna-to-receiver ports ([Formula: see text]), within a frequency band of 2.2–4.6 GHz. The isolation between the transmitter and the receiver ports ([Formula: see text]) is better than 24 dB with a maximum value of 29.5[Formula: see text]dB @ 3.6[Formula: see text]GHz. The power dissipation of the proposed AQC is 40[Formula: see text]mW and it covers an active chip area of 0.677[Formula: see text]mm2.
Underwater Image Enhancement Using a Multiscale Dense Generative Adversarial Network

Underwater image enhancement has received much attention in underwater vision research. However, raw underwater images easily suffer from color distortion, underexposure, and fuzz caused by the underwater scene. To address the above-mentioned problems, we propose a new multiscale dense generative adversarial network (GAN) for enhancing underwater images. The residual multiscale dense block is presented in the generator, where the multiscale, dense concatenation, and residual learning can boost the performance, render more details, and utilize previous features, respectively. And the discriminator employs computationally light spectral normalization to stabilize the training of the discriminator. Meanwhile, nonsaturating GAN loss function combining $L_1$ loss and gradient loss is presented to focus on image features of ground truth. Final enhanced results on synthetic and real underwater images demonstrate the superiority of the proposed method, which outperforms nondeep and deep learning methods in both qualitative and quantitative evaluations. Furthermore, we perform an ablation study to show the contributions of each component and carry out application tests to further demonstrate the effectiveness of the proposed method.