Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Scale Identification of Nucleosome Positions in S. cerevisiae

The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. We developed a tiled microarray approach to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions. The majority of the nucleosomes identified were well-positioned. We found a stereotyped chromatin organization at Pol II promoters consisting of a nucleosome-free region ∼200 base pairs upstream of the start codon flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved and were enriched in poly-deoxyadenosine or poly-deoxythymidine sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.
Outage analysis for adaptive two-way relaying

This paper analyzes the outage performance of cooperative protocols for the two-way relaying model in which a halfduplex relay assists in the bi-directional communications of two terminals. We first define the outage events of conventional nonadaptive Amplify-and-Forward (AF) and Decode-and-Forward (DF) two-way relaying protocols and derive closed form results for their respective outage probabilities. Then we propose a simple adaptive protocol which switches between AF and DF depending on the number of data streams successfully decoded at the relay. We derive the outage probability for this adaptive scheme in closed form and show that it outperforms the nonadaptive schemes. It is noted that the closed form results are applicable to arbitrary channel gains between terminals.
From differential equations to differential geometry: aspects of regularisation in machine learning

Machine learning requires the use of prior assumptions which can be encoded into learning algorithms via regularisation techniques. In this thesis, we examine in three examples how suitable regularisation criteria can be formulated, what their meaning is, and how they lead to efficient machine learning algorithms. Firstly, we describe a joint framework for positive definite kernels, Gaussian processes, and regularisation operators which are commonly used objects in machine learning. With this in mind, it is then straightforward to see that linear differential equations are an important special case of regularisation operators. The novelty of our description is the broad, unifying view connecting kernel methods and linear system identification. We then discuss Bayesian inference and experimental design for sparse linear models. The model is applied to the task of gene regulatory network reconstruction, where the assumed network sparsity improves reconstruction accuracy and our proposed experimental design setup outperforms prior methods significantly. Finally, we examine non-parametric regression between Riemannian manifolds, a topic that has received little attention so far. We propose a regularised empirical risk minimisation framework, ensuring with the help of differential geometry that it does not depend on the representation of the input and output manifold. We apply our approach to several practical learning tasks in robotics and computer graphics. A priori Annahmen sind fur das maschinelle Lernen unabdingbar, und eine Moglichkeit, diese Annahmen in Lernalgorithmen zu kodieren, ist die Regularisierung. In dieser Dissertation wird anhand von drei Beispielen untersucht, wie man sinnvolle Regularisierungskriterien formulieren kann und wie daraus effiziente Lernalgorithmen entstehen. Zuerst werden Zusammenhange zwischen positiv definiten Kernen, Gausprozessen und Regularisierungsoperatoren, wie sie haufig im maschinellen Lernen verwendet werden, beschrieben. Dabei wird klar, dass lineare Differentialgleichungen einen wichtigen Spezialfall solcher Operatoren darstellen, und dass Kernmethoden daher eng mit der linearen Systemidentifikation verwandt sind. Danach wird Bayessche Inferenz und Versuchsplanung in dunnbesetzten, linearen Modellen diskutiert. Das Modell wird auf die Rekonstruktion von genetischen Interaktionsnetzwerken angewendet. Durch die Annahmne, dass die zu schatzenden Vektoren dunnbesetzt sind, und durch die neuartige Versuchsplanungsmethode ergeben sich signifikante Verbesserungen der Rekonstruktion. Schlieslich wird nichtparametrische Regression zwischen Riemannschen Mannigfaltigkeiten mittels regularisierter, empirischer Risikominimierung untersucht. Es wird darauf geachtet, dass die Regularisierung unabhangig von der Darstellung der Mannigfalitgkeiten ist. Die vorgestellte Methode wird anhand verschiedener Beispiele aus der Robotik und der Computergraphik getestet.
Inside the "Black Box": Investigating the Link between Organizational Readiness and IT Implementation Success

The complexity of today’s organizational IT-driven transformations, such as implementing ERPs and CRMs, urges companies to conduct upfront preparations to ensure implementation success. Organizational readiness is therefore regarded as a critical precondition that increases the chances of IT implementation success. To deepen the theoretical understanding of the link between organizational readiness and IT implementation success, we present preliminary results of a qualitative survey among a group of seasoned IT project/change management experts and derive a theoretical framework explaining the link between the two constructs.
Joint Energy Harvesting and Jamming Design in Secure Communication of Relay Network

This paper investigates the secrecy performance of amplified-and-forward (AF) relay wiretap model by using energy harvesting (EH) and signal alignment technique. All nodes equipped with multi antennas play different roles in terms of source, destination, relay, eavesdropper and jamming node. The jamming node designs artificial noise based on signal alignment principle, and then transmits it to the eavesdropper with harvested energy. Due to different power limitations, we propose power allocation schemes called Local Power Constraints scheme (LPCS) and Global Power Constraints scheme (GPCS), which maximize the secrecy rate of the system and obtain better secrecy performance when compared with the non-EH scheme and the partial nodes power allocation EH scheme. Furthermore, we also analyze the effect of the energy harvesting on the secure degrees of freedom (SDOF) in the high signal-to-noise (SNR) region, and simulate the secrecy performance with convex optimization method by proving the convexity of the optimization problem. Results show that the proposed schemes outperform the compared schemes on the secrecy performance, and achieve more secrecy rate when the destination and the relay have more antennas.
Significance of the changes in the respiratory system pressure-volume curve during acute lung injury in rats.

UNLABELLED The hypothesis that the changes in the respiratory system pressure- volume (PV) curve during pulmonary edema mainly reflect distal airway obstruction was investigated in rats. Normal rats had a well-defined upper inflection point (UIP) at low airway pressure. Airway occlusion by liquid instillation decreased compliance (Crs) and the volume (Vuip) of the UIP, and increased end-inspiratory pressure. The same changes were observed during the progression of edema produced by high volume ventilation (HV). Changes in Vuip and in Crs produced by HV were correlated with edema severity in normal rats or rats with lungs preinjured with alpha-naphthylthiourea. Vuip and Crs changes were proportional, reflecting compression of the PV curve on the volume axis and suggesting reduction of the amount of ventilatable lung at low airway pressure. In keeping with this explanation, the lower Vuip and Crs were before HV, the more severe HV-induced edema was in alpha-naphthylthiourea-injected rats. When edema was profuse, PV curves displayed a marked lower inflection point (LIP), the UIP at low pressure disappeared but another was seen at high volume above the LIP, and the correlation between Vuip changes and edema severity was lost. These observations may have clinical relevance in the context of the "open lung" strategy. KEYWORDS ventilator-induced lung injury; respiratory mechanics; acute respiratory distress syndrome
Effects of dietary particulate limestone, vitamin K3 and fluoride and photostimulation on skeletal morphology and osteoporosis in laying hens

1. Female chicks of a White Leghorn strain were fed three different diets from one day old: control, additional vitamin K3 (10 mg/kg), and a diet containing a combination of additional vitamin K3, sodium fluoride (10 mg/kg) and limestone in particulate rather than powdered form. At 16 weeks photoperiod was increased for half the birds from 8:16 L:D to 16:8 L:D immediately or by one hour per week to the same ultimate photoperiod for the other half. 2. Age at first egg was lower by 4·0 d for birds on the fast lighting regime but there were no overall effects of lighting on bone quality at either 25 or 70 weeks. 3. Additional vitamin K3 resulted in higher proximal tarsometatarsus cancellous bone volumes at 15 weeks and throughout the laying period compared with controls. Plasma osteocalcin concentrations were unaffected by vitamin K3 supplementation during growth. 4. The combination diet resulted in beneficial responses of 12 to 20% in most bone characteristics in hens at 70 weeks. The magnitude of these effects was similar to a previous study involving a particulate calcium source alone (Fleming et al., Poultry Science, 39: 434–440, 1998 b). We conclude that the beneficial effects of the combined treatment over the lifetime of the hens were attributable mainly to the presence in the diet of a calcium source in particulate form.
Propagation Characteristics of Mobile Channel in Urban Micro-Cells at 3.5 GHz and 6 GHz

In this paper, the mobile channel propagation measurements at 3.5 GHz and 6 GHz have been performed in urban micro-cell scenario in the city of China. The measured cases include line-of-sight (LOS) and non- line-of-sight (NLOS) propagation. Statistical results and comparative analysis are presented in this paper, including power delay profiles (PDPs), path loss (PL), coverage, and root mean square (rms) delay spread (DS). It can be found that PDPs measured from campaign keep similarity in these two bands. The result based on PDPs demonstrates that, in mobile condition, the PL exponent of 6 GHz is a little greater than that of 3.5 GHz in both LOS and NLOS propagation. Moreover, as the frequency increases, the path loss will increase and the coverage will remarkably degrade. Last, the rms DS of 3.5 GHz and 6 GHz are similar in LOS case, while that of 3.5 GHz is higher in NLOS case.
Measuring operative performance after laparoscopic skills training: edited videotape versus direct observation.

BACKGROUND AND PURPOSE Global assessment by direct observation has been validated for evaluating operative performance of surgery residents after formal skills training but is time-consuming. The purpose of this study was to compare global assessment performed from edited videotape with scores from direct observation. MATERIALS AND METHODS Junior surgery residents (N = 22) were randomized to 2 weeks of formal videotrainer skills training or a control group. Laparoscopic cholecystectomy was performed at the beginning and end of the rotation, and global assessment scores were compared for the training and control groups. Laparoscopic videotapes were edited: initial (2 minutes), cystic duct/artery (6 minutes), and fossa dissection (2 minutes). Two independent raters performed both direct observation and videotape assessments, and scores were compared for each rater and for interrater reliability using a Spearman correlation. RESULTS Correlation coefficients for videotape versus direct observation for five global assessment criteria were <0.33 for both raters (NS for all values). The correlation coefficient for interrater reliability for the overall score was 0.57 (P = 0.01) for direct observation v 0.28 (NS) for videotape. The trained group had significantly better overall performance than the control group according to the assessment by direct observation (P = 0.02) but not by videotape assessment (NS). CONCLUSIONS Direct observation demonstrated improved overall performance of junior residents after formal skills training on a videotrainer. Global assessment from an edited 10-minute videotape did not correlate with direct observation and had poor interrater reliability. Efficient and valid methods of evaluating operative performance await development.
Dose of Trimethoprim-Sulfamethoxazole To Treat Skin and Skin Structure Infections Caused by Methicillin-Resistant Staphylococcus aureus

ABSTRACT We undertook this study to investigate whether treatment with a higher dose of trimethoprim-sulfamethoxazole (TMP/SMX) led to greater clinical resolution in patients with skin and soft tissue infections (SSTIs) caused by methicillin-resistant Staphylococcus aureus (MRSA). A prospective, observational cohort with nested case-control study was performed at a public tertiary health system. Among patients with MRSA SSTIs during the period from May 2008 to September 2008 who received oral monotherapy with TMP/SMX and whose clinical outcome was known, the clinical characteristics and outcomes were compared between patients treated with a high dose of TMP/SMX (320 mg/1,600 mg twice daily) for 7 to 15 days and patients treated with the standard dose of TMP/SMX (160 mg/800 mg twice daily) for 7 to 15 days. In patients with MRSA SSTIs, those treated with the high dose of TMP/SMX (n = 121) had clinical characteristics similar to those of patients treated with the standard dose of TMP/SMX (n = 170). The only exception was a higher proportion of patients with a history of trauma upon admission among the patients treated with the higher dose. The proportion of patients with clinical resolution of infection was not different in the two groups (88/121 [73%] versus 127/170 [75%]; P = 0.79). The lack of significance remained in patients with abscess upon stratified analysis by whether surgical drainage was performed. The study found that patients with MRSA SSTIs treated with the higher dose of TMP/SMX (320/1,600 mg twice daily) for 7 to 15 days had a similar rate of clinical resolution as patients treated with the standard dose of TMP/SMX (160/800 mg twice daily) for 7 to 15 days.
CONTROLLING TCAD APPLICATIONS WITH A DYNAMIC DATABASE

State-of-the-art TCAD applications like device and process simulators require a huge number of parameters to control the various simulation modes and models. Simple input deck files which are just a sequence of static keywords or the use of the command line are no longer sufficient. Since the values and the usage of these parameters depend on each other it is mandatory to utilize mathematical expressions and hierarchical dependencies. We present an approach which relies on an object-oriented dynamic database to control the simulators. The database provides keywords grouped in sections which can be nested and inherited to build arbitrary hierarchies. For optimal control over the simulation, the contents of the database can be dynamically adapted using runtime information provided by the simulators like update norms, iteration counters and related information.
Cochlear Implantation at under 12 months: Report on 10 Patients

Objectives: There is growing evidence that early application of a cochlear implant in children affected by profound congenital hearing loss is of paramount importance for the development of an adequate auditory performance and language skills. For these reasons and as a result of advances in audiologic diagnosis and an enhanced awareness of the safety of cochlear implants, the age of implantation has substantially decreased over recent years. Children aged as little as 12 months are now being implanted in some centers. On the basis of our experience with very young children, we believe that the date of implantation may be further reduced to only 4 to 6 months of age.
Impact of Patient Compliance on Tooth Loss during Supportive Periodontal Therapy

Periodontal treatment consists of active periodontal therapy (APT) and supportive periodontal therapy (SPT). Regular SPT is recommended to prevent and control the occurrence of periodontal disease following APT. A patient’s compliance with SPT is considered one of the most important factors affecting long-term periodontal status. Tooth loss is generally considered the final outcome of periodontitis. This review aimed to analyze the relationship between patient compliance with regular SPT and tooth loss. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guideline for systematic reviews was used. A search of articles was conducted using MEDLINE (PubMed) and other databases. Quality assessments of selected studies were performed. To assess the effect of compliance on tooth loss during SPT, pooled risk ratio of tooth loss (RRTL) was used as the primary outcome. Pooled risk difference of tooth loss (RDTL) and weighted mean difference of tooth loss rate (WDTLR) were used as secondary outcomes. Subgroup analysis and meta-regression were conducted to evaluate the effects of different variables. In total, 710 articles were screened. Eight studies, which had a regular-compliance (RC) group and an erratic-compliance (EC) group with at least a 5-y follow-up period, qualified for the meta-analysis. The risk of tooth loss in the RC group was significantly lower than that in the EC group (pooled RRTL: 0.56 [confidence interval (CI): 0.38, 0.82]; pooled RDTL: –0.05 [CI: –0.08, –0.01]). The definition of compliance was a variable significantly related to risk ratio of tooth loss. Patients in the RC group had significantly lower tooth loss rate during SPT than did patients in the EC group (WDTLR: –0.12 [CI: –0.19, –0.05]). Teeth have less risk of being lost if patients are more compliant with supportive periodontal therapy. However, unidentified variables causing data heterogeneity and affecting the risk of tooth loss may have been present. More well-controlled prospective studies are needed in the future.
Hardware acceleration of a face detection system on FPGA

Face detection is a computer technology that has been used in various applications such as biometric authentication, surveillance, computer interaction and social media. It is the process of detecting faces in an image or video stream and is an important step that precedes face recognition. Many researchers in recent years are implementing real time and accurate face detection system on FPGA due to computing resource and design flexibility. This paper presents an implementation of a face detection system accelerated on FPGA for high throughput. The proposed system utilizes stream-oriented hardware architecture to perform image pre-processing, skin segmentation, filtering as well as connected component labeling processes. Window-based image processing such as median and morphological filtering were accelerated using line buffering technique to achieve maximum throughput. The detection system was implemented on an Altera Cyclone IV FPGA and was benchmarked against a software implementation using NIOS II soft-core processor. The hardware design achieved a speed-up of 250 times compared to software implementation when processing a RGB video frame of 800×600 pixel size.
Human Immunodeficiency Virus Type 1 T-Lymphotropic Strains Enter Macrophages via a CD4- and CXCR4-Mediated Pathway: Replication Is Restricted at a Postentry Level

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) laboratory strains adapted to T-cell lines, as well as most syncytium-inducing primary isolates, replicate poorly in macrophages, which, beside CD4+ T lymphocytes, are major targets of HIV-1. In the present work, we used a semiquantitative PCR-based technique to study viral entry into cells, kinetics of reverse transcription, and translocation of the viral DNA into the nucleus of macrophages infected with different HIV-1 strains. Our results demonstrate that T-lymphotropic strains efficiently enter macrophages. Entry was inhibited by a monoclonal antibody against CD4 and by stromal cell-derived factor 1α, a natural ligand of CXCR4, suggesting that both CD4 and CXCR4 act as receptors on macrophages for HIV-1 T-lymphotropic strains. Analysis of the kinetics of reverse transcription and nuclear import revealed that the most pronounced differences between T-lymphotropic and macrophagetropic strains occurred at the level of nuclear translocation of viral DNA, although a delay in reverse transcription was also observed. These results suggest that postentry steps are critical for restricted replication of T-lymphotropic HIV-1 strains in macrophages.
PHYSICAL SPOUSAL VIOLENCE AGAINST WOMEN IN INDIA: SOME RISK FACTORS

Summary Domestic spousal violence against women in developing countries like India, is now beginning to be recognized as a widespread health problem impeding development. This study aimed to explore the risk and protective factors for lifetime spousal physical violence. A cross-sectional household survey was carried out in rural, urban and urban-slum areas across seven sites in India, among women aged 15–49 years, living with a child less than 18 years of age. The sample was selected using the probability proportionate to size method. Trained field workers administered a structured questionnaire to elicit information on spousal physical violence. The main hypothesized variables were social support, witnessed father beating mother and experience of harsh physical violence during childhood, alcohol abuse by spouse and socioeconomic variables. The outcome variables included three physical violence behaviours of hit, kick and beat. Odds ratios were calculated for risk and protective factors of violence using logistic regression. Of 9938 women surveyed, 26% reported experiencing spousal physical violence during the lifetime of their marriage. Adjusted odds ratios calculated using multiple logistic regression analysis suggest that women whose husbands regularly consumed alcohol (OR 5·6; 95% CI 4·7–6·6); who experienced dowry harassment (OR 3·2; 95% CI 2·7–3·8); had reported experiencing harsh physical punishment during childhood (OR 1·6; 95% CI 1·4–1·8) and had witnessed their fathers beat their mothers (OR 1·9; 95% CI 1·6–2·1), were at increased risk of spousal physical violence (beat, hit and kick). Higher socioeconomic status and good social support acted as protective buffers against spousal physical violence. The findings provide compelling evidence of the potential risk factors for spousal physical violence, which in turn could help in planning interventions.