Miracle-dz/UniFAR-FTUs huggingface dataset:
Involvement of the RNA polymerase II-associated Paf1 complex in transcriptional regulation and 3'-end formation of snoRNAs

Transcription elongation is an important regulatory step in the RNA polymerase II transcription cycle. Previous work from our laboratory and others strongly suggests that the Paf1 complex interacts with and regulates the activity of RNA polymerase II during transcription elongation. Affinity purification of Paf1 revealed that it exists in a complex in vivo with Ctr9, Rtf1, Cdc73 and Leo1 called the Paf1 complex. To further investigate the function of the Paf1 complex in vivo, we used a genetic approach to study the component Rtf1 and microarray analyses to identify Ctr9-regulated genes. Null mutations in RTF1 confer two phenotypes associated with defective transcription elongation, sensitivity to base analogs and the Spt- phenotype. To identify novel mutations in RTF1, we performed a genetic screen for rtf1 mutations that confer conditional mutant phenotypes. We identified three new rtf1 missense mutations. To identify proteins that functionally interact with the Paf1 complex, we performed a screen for multicopy suppressors of the rtf1 mutations. This screen identified NAB3 as a suppressor of rtf1. Nab3 interacts with the RNA polymerase II-associated hnRNP Nrd1. Together, Nrd1 and Nab3 are required for efficient 3'-end formation of certain nonpolyadenylated RNA polymerase II transcripts, including snoRNAs. Using assays to detect transcriptional readthrough of snoRNA genes, we have shown that deletion of certain Paf1 complex members causes strong defects in snoRNA 3'-end formation. By chromatin immunoprecipitation (ChIP) analysis, we have found that the Paf1 complex and Nab3 associate with snoRNA genes in vivo. In the second approach, expression analyses revealed a role for the Paf1 complex in directly regulating the expression of certain genes that are not transcribed during growth in rich media. ChIP experiments indicated that the Paf1 complex associates along the length of ARG1 and with the promoter region of SER3. Together, our results reinforce the idea that the Paf1 complex is involved in the production of mRNAs and provide evidence that the Paf1 complex also participates in snoRNA transcription and 3'-end formation during RNA polymerase II transcription.
Evaluating Online Consumer Medication Information Systems: Comparative Online Usability Study

Background Medication is the most common intervention in health care, and the number of online consumer information systems within the pharmaceutical sector is increasing. However, online consumer information systems can be a barrier for users, imposing information asymmetries between stakeholders. Objective The objective of this study was to quantify and compare the usability of an online consumer medication information system (OCMIS) against a reference implementation based on an interoperable information model for patients, physicians, and pharmacists. Methods Quantitative and qualitative data were acquired from patients, physicians, and pharmacists in this online usability study. We administered 3 use cases and a post hoc questionnaire per user. Quantitative usability data including effectiveness (task success), efficiency (task time), and user satisfaction (system usability scale [SUS]) was complemented by qualitative and demographic data. Users evaluated 6 existing systems and 1 reference implementation of an OCMIS. Results A total of 137 patients, 81 physicians, and 68 pharmacists participated in this study. Task success varied from 84% to 92% in patients, 66% to 100% in physicians, and 50% to 91% in pharmacists. Task completion time decreased over the course of the study for all but 2 OCMIS within the patient group. Due to an assumed nonnormal distribution of SUS scores, within-group comparison was done using the Kruskal-Wallis test. Patients showed differences in SUS scores (P=.02) and task time (P=.03), while physicians did not have significant differences in SUS scores (P=.83) and task time (P=.72). For pharmacists, a significant difference in SUS scores (P<.001) and task time (P=.007) was detected. Conclusions The vendor-neutral reference implementation based on an interoperable information model was proven to be a promising approach that was not inferior to existing solutions for patients and physicians. For pharmacists, it exceeded user satisfaction scores compared to other OCMIS. This data-driven approach based on an interoperable information model enables the development of more user-tailored features to increase usability. This fosters data democratization and empowers stakeholders within the pharmaceutical sector.
The distraction hypothesis depends on relatively cheap extrafloral nectaries

Extrafloral nectaries may have evolved because they distract insects from flowers. For this to have occurred, extrafloral nectaries must be cheaper than flowers. This requirement stands in addition to the requirement thatextrafloral nectaries must reduce the rate of insect visits to flowers. In the model examined here, the cost of each extrafloral nectary divided by the cost of each flower must be less than the proportion of reproduction threatened by insect visits.
Addressing Irregularity in Sparse Neural Networks Through a Cooperative Software/Hardware Approach

Neural networks have become the dominant algorithms rapidly as they achieve state-of-the-art performance in a broad range of applications such as image recognition, speech recognition, and natural language processing. However, neural networks keep moving toward deeper and larger architectures, posing a great challenge to hardware systems due to the huge amount of data and computations. Although <italic>sparsity</italic> has emerged as an effective solution for reducing the intensity of computation and memory accesses directly, irregularity caused by sparsity (including sparse synapses and neurons) prevents accelerators from completely leveraging the benefits, i.e., it also introduces costly indexing module in accelerators. In this article, we propose a cooperative software/hardware approach to address the irregularity of sparse neural networks efficiently. Initially, we observe the local convergence, namely larger weights tend to gather into small clusters during training. Based on that key observation, we propose a software-based coarse-grained pruning technique to reduce the irregularity of sparse synapses drastically. The coarse-grained pruning technique, together with local quantization, significantly reduces the size of indexes and improves the network compression ratio. We further design a multi-core hardware accelerator, Cambricon-SE, to address the remaining irregularity of sparse synapses and neurons efficiently. The novel accelerator have three key features: 1) <italic>selector modules</italic> to filter unnecessary synapses and neurons, 2) <italic>compress/decompress modules</italic> for exploiting the sparsity in data transmission (which is rarely studied in previous work), and 3) a <italic>multi-core architecture</italic> with elevated throughput to meet the real-time processing requirement. Compared against a state-of-the-art sparse neural network accelerator, our accelerator is <inline-formula><tex-math notation="LaTeX">$1.20 \times$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>1</mml:mn><mml:mo>. </mml:mo><mml:mn>20</mml:mn><mml:mo>×</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="xi-ieq1-2978475.gif"/></alternatives></inline-formula> and <inline-formula><tex-math notation="LaTeX">$2.72 \times$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>2</mml:mn><mml:mo>. </mml:mo><mml:mn>72</mml:mn><mml:mo>×</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="xi-ieq2-2978475.gif"/></alternatives></inline-formula> better in terms of performance and energy efficiency, respectively. Moreover, for real-time video analysis tasks, Cambricon-SE can process 1080p video at the speed of 76.59 fps.
Expression Analysis of Cytoskeletal and Ribosomal Genes during Adult Diapause in the Northern House Mosquito, Culex pipiens

The cDNA encoding beta-tubulin in the mosquito Culex pipiens has high similarity with the beta-tubulins reported in other insects. In this study, we examine expression of this gene and microtubule abundance in relation to diapause and low temperature. While nondiapausing mosquitoes express beta-tubulin highly in their thoracic muscles, expression is quite low during adult diapause. The abundance of microtubules was also much lower in flight muscles of diapausing adults than in flight muscles from nondiapausing individuals, as confirmed by laser confocal microscopy of tubulins stained using indirect immunofluorescence. Low temperature decreased microtubule abundance in midguts of nondiapausing mosquitoes, but microtubule abundance in diapausing mosquitoes was already low and remained unchanged by low temperature exposure. Overall, pixel intensity averages were higher in the flight muscles than in the midguts, and again low temperature decreased microtubule abundance in the flight muscles of nondiapausing females,
Contextual Cues for Causal Visual Tracking

As a consequence of the ever increasing automation, many application domains – such as autonomous driving or visual surveillance – have to deal with vast amounts of visual data. Efficient data processing and subsequent reasoning about the ongoing events requires automated video analysis. An essential requirement for such automated analysis is to accurately localize objects and reliably estimate their trajectories over time, in order to deduce which (inter-)actions are observed by a camera. To address these tasks, numerous visual object tracking paradigms have been investigated over the past few decades. The majority of these approaches, however, focuses only on the dynamics and visual representation of the target itself, neglecting the information gain provided by other contextual cues which are readily available from the recorded visual data. In this thesis, we investigate the potential of auxiliary scene information, i.e. context, to robustify visual object tracking. To this end, we exploit often neglected information sources to build intuitive, yet very accurate and efficient tracking models. These models cover both appearance-based and geometric context to address several limitations of existing work. Appearance, on the one hand, can be used to reduce the risk of drifting in the case of visually ambiguous scenarios. Leveraging geometric prior knowledge and observed scene dynamics, on the other hand, allows to model plausible movements of missed or otherwise undetected objects which can be exploited to resolve occlusions. We rely on these context cues to build causal visual object trackers, which are suitable for time-critical applications. To demonstrate both the benefits and limitations of each context-aware model, we conduct detailed evaluations on challenging real-world test scenarios. This work was partially supported by the Austrian Science Foundation (FWF) via the project Advanced Learning for Tracking and Detection in Medical Workflow Analysis (I535-N23). The GeForce © Titan Xp used for parts of this research was donated by the NVIDIA © Corporation. I gratefully do not thank reviewer B for regularly rejecting our grant applications which wasted time we could not spend on research.
COMPARATIVE STUDY ON THE EVALUATION OF TEMPOROMANDIBULAR JOINT AND NECK STRUCTURES IN HEALTHY VOLUNTEERS AND IDIOPATHIC SCOLIOSIS PATIENTS

Objective: The aim of this study was to investigate the correlation of temporomandibular joint disorders (TMD) and neck structure changes in adolescents with idiopathic scoliosis (IS) by clinical examination. Material and Methods: The study included 51 patients affected by IS (24 males, 27 females; mean age: 13.5 ± 2.1 years) selected using simple random sampling, and a healthy control group of 50 subjects (23 males, 27 females; mean age: 14.5 ± 2.3 years). The Diagnostic Criteria for Temporomandibular Disorders: Clinical Protocol and Assessment Instruments (DC/TMD) form was utilized to assess the signs and symptoms of TMD in the subjects. For the evaluation of neck structures, masseter and temporalis muscles, pressure pain threshold (PPT) values were measured with a hand-held pressure algometer. Obtained data were analyzed statistically applying Mann-Whitney U test, Wilcoxon, and chi-squared tests with a significance level of 0.05. Results: According to the DC/TMD form, the following parameters showed statistically significant differences between the groups (p 0.001): presence of TMD, temporal headache, midline deviation, and right and left lateral movements. The PPT values were higher in the control group compared with the study group (p < 0.001). Additionally, the type of pain-related TMD identified in the subjects was myalgia. The myalgia was significantly (p < 0.001) higher in the study group (68.6%) than in the control group (22%). Conclusion: This study concluded that spinal diseases which cause postural changes, like IS, in the head and shoulder region are associated with muscle adaptation and alterations in the temporomandibular joint area.
Prenatal Exposure to Organophosphate Pesticides in Vojvodina

Introduction: Organophosphate pesticides (OPs) are commonly used pesticides which are metabolized and excreted in urine. There are many studies reporting the levels of OP metabolites in urine of pregnant women from different countries, but there is no published data on this problem in Serbia. Aims: The aim of this study was to determine the level of OP pesticide exposure of pregnant women in the Vojvodina region, Serbia. Methods: Sixty healthy pregnant women were recruited to participate in this study. A trained interviewer administered a questionnaire to each woman. The concentrations of five Original Research Article Živković et al.; JAMMR, 28(7): 1-13, 2018; Article no.JAMMR. 46101 2 dialkylphosphate metabolites of the organophosphorus pesticides were determined in urine samples that were taken on the third postpartum day. Fifty-eight maternal urine samples were collected. Results: Approximately two thirds (65.5%) of pregnant women reported living in urban areas and rest living in rural areas. The number of positive urine samples varied from 65.5% for dimethylphosphate (DMP) to 34.5% for diethyldithiophosphate (DEDTP). The mean urine concentrations were highest for DMP (5.714 μg/L cre). Other metabolite concentrations averaged around 1 μg/L cre. Conclusions: This study confirms prenatal exposure to OP pesticides in the Vojvodina region, Serbia. Levels of dialkylphosphate metabolites in pregnant women from Serbia are comparable with those reported for Caribbean countries and the Palestinian region.
Remote Operation of Unmanned Surface Vessel through Virtual Reality

An unmanned ship can be designed without considering humancomfort, and can thus be constructed lighter, smaller and less expensive.It can carry out missions in rough terrain or be in areaswhere it would be dangerous for a human to operate. By not havingto support a crew, lengthy missions can be accepted, enabling, e.g.reconnaissance missions, or reducing emissions by lowering thespeed.Breakthroughs with autonomous systems enable more advancedunmanned surface vessels (USVs), but to be able to handle complexmissions in a dynamic environment, a human operator is stillassumed an effective decision maker. Thus, we propose a methodfor remote operation of a USV, where the operator uses VirtualReality (VR) to comprehend the surrounding environment. Greatimportance has been given to the ability to perform safe navigation,by designing a Graphical User Interface (GUI) that guides the operatorthrough the navigation process, by presenting the importantinformation at the right place in the right orientation. (Less)
Four-dimensional model: a literature review in online organisational knowledge sharing

Purpose Online knowledge sharing is a popular activity worldwide and can be leveraged by organisations to innovate, create and sustain competitive advantage. Although there have been a number of studies examining knowledge sharing to encourage employees to convey their skills and experiences to others in an organisation, few attempts have been made to investigate the key motivators of online knowledge sharing in an organisation. Based on the theory of planned behaviour and technological acceptance model, this study aims to review the literature to establish a conceptual framework examining motivators of online knowledge sharing in organisations. Design/methodology/approach Previous studies that investigated motivators of online knowledge sharing in organisations in the literature were reviewed to propose a conceptual framework. Findings Four-dimensional model, which includes four types of key motivators of online knowledge sharing, namely, individual, social, organisational and technological, was established. Originality/value The model serves as a roadmap for future researchers and managers considering their strategy to enhance online knowledge sharing in organisations.
OPTIMUM POWER SCHEDULING FOR DEMAND SIDE MANAGEMENT IN SMART GRID PARADIGM

High-tech advances in the field of domestic appliances and industrial automations of recent times have caused an aggravated electricity demand. The conversion of many manual and fossil fuel powered appliances into electric powered devices, e.g. Plug-in electrical vehicles (PEV) (Deilami et al. 2011), is also causing escalation in the power needs. Conventional power grids are progressing into smarter versions called smart grid (SG). SG requires power scheduling of consumer devices when the power requirement is raised; this process is known as demand response (DR). Demand response (DR) in a SG paradigm requires consumers to shift their loads to time slots of low power usage, which benefits both consumer and electricity supply company (ESC) in terms of reduced expenditures. Domestic consumers can gain cost reduction benefit by scheduling their device activation time (DAT) towards the slots of low charge. Consumer can decrease their energy expenses by participating in DR events which results in a reduction in the peak-to-average (PAR) of whole system. Power Scheduling is one of the vital solutions to ensure reliability and stability of SG. Power scheduling systems for domestic consumer appliances/devices are usually referred to as home energy management system (HEMS) (Kim et al., 2015). As a significant component of the SG, HEMS has become increasingly imperative, because electricity usage of domestic sector contributes for a substantial amount of total electricity consumption. Minimization in cost is essential in home energy management systems (HEMS) to induce consumers acceptance for power scheduling to accommodate for a DR at peak hours. Many proposed algorithms addressed
The Interactive Ecology of Juvenile Atlantic Salmon and Smallmouth Bass: Competition for Habitat

Exotic smallmouth bass have invaded much of the historic freshwater habitat of Atlantic salmon in North America, yet little is known about ecological interactions between the two species. We investigated the possibility of competition for habitat between Atlantic salmon and smallmouth bass using two in situ experiments. We used snorkel observation to identify the degree and timing of overlap in habitat use and to describe habitat shifts by Atlantic salmon in the presence of smallmouth bass. In late July, 2008, we observed substantial overlap in depths and mean water column velocities used by both species in sympatry, and an apparent shift by age 0 Atlantic salmon to shallower water coinciding with the period of high overlap. We detected no overlap or habitat shifts by age 0 Atlantic salmon in the presence age 1 smallmouth bass, and low overlap and no habitat shifts of Atlantic salmon and age 0 smallmouth bass in fall 2008. Summer floods of 2009, with sustained high flows and low temperatures, resulted in a near complete reproductive failure of smallmouth bass in our study streams, thus compromising our ability to replicate our 2008 experiments. We suggest that environmental conditions of temperature and discharge mediate interactions of these species, and thus determine the outcomes of potential competition.
Sparse Methods for Learning Multiple Subspaces from Large-scale, Corrupted and Imbalanced Data

In many practical applications in machine learning, computer vision, data mining and information retrieval one is confronted with datasets whose intrinsic dimension is much smaller than the dimension of the ambient space. This has given rise to the challenge of effectively learning multiple low-dimensional subspaces from such data. Multi-subspace learning methods based on sparse representation, such as sparse representation based classification (SRC) and sparse subspace clustering (SSC) have become very popular due to their conceptual simplicity and empirical success. However, there have been very limited theoretical explanations for the correctness of such approaches in the literature. Moreover, the applicability of existing algorithms to real world datasets is limited due to their high computational and memory complexity, sensitivity to data corruptions as well as sensitivity to imbalanced data distributions. This thesis attempts to advance our theoretical understanding of sparse representation based multi-subspace learning methods, as well as develop new algorithms for handling large-scale, corrupted and imbalanced data. The first ii
Production and characterization of SulP anion transporters

The main subject of this thesis is the Sulphate Permease (SulP) protein family that includes more than two hundred members, identified in archaea, bacteria, fungi, plants and animals. Many of these proteins have been functionally characterized: most are anion exchangers or transporters with different substrate specificities and distinct mechanism of action (Saier et al., 1999). In mammals, the SulP family, known as Solute Linked Carrier 26 (SLC26), is composed of eleven members with important roles in normal physiology (Mount and Romero, 2004). The SulP proteins show a similar structural organization: a hydrophobic central core, which includes ten or twelve membrane helixes, and a less conserved C-terminal cytoplasmic portion that includes a STAS domain (Sulphate Transporter and Anti-Sigma factor antagonist domain). Despite the functional role of the STAS domain is still unclear, it appears to be crucial for the regulation of the transport activity (Ko et al., 2004; Zheng et al., 2005; Shibagaki and Grossman, 2006). Its fundamental role is also underlined by the fact that mutations that alter this domain in the SLC26 family can cause loss of function, resulting in serious genetic diseases, like diastrophic dysplasia or Pendred syndrome (Dawson and Markovich, 2005). No three-dimensional structure of STAS domains or full-length sequences is available for any SulP anion transporter. One part of the work was focused on the production of different forms of the STAS domain from different species, for the biophysical and structural characterization. Another part of the SulP project was performed at the Johann Wolfgang Goethe University of Frankfurt (Germany) and aimed at the production of some full-length SulP proteins, by a cell-free expression system, an emerging technique for the large-scale production of membrane proteins. In the last year, I was also involved in the crystallographic study of the Green Fluorescence Protein mutant, GFPmut2, in collaboration with Prof. Stefano Bettati of the University of Parma (Italy). The main aim of this work was the elucidation of the structural basis of the spectroscopic properties of this mutant, in particular with respect to changes in pH. The GFP chromophore can, in fact, exist either in a protonated or deprotonated state, with distinct spectral properties (Tsien, 1998). In a previous spectroscopic characterization, GFPmut2 (Ser65Ala, Val68Leu, Ser72Ala) was found more sensitive than the wild type GFP to pH changes in the physiological range (Chirico et al., 2002). The structures of GFPmut2 at pH 6 and pH 9 were determined at around 1.6 A resolution, allowing the correlation between the spectral and structural properties.