Miracle-dz/UniFAR-FTUs huggingface dataset:
Sperm count as a surrogate endpoint for male fertility control

When assessing the effectiveness of a hormonal method of fertility control in men, the classical approach used for the assessment of hormonal contraceptives in women, by estimating the pregnancy rate or using a life‐table analysis for the time to pregnancy, is difficult to apply in a clinical development program. The main reasons are the dissociation of the treated unit, i.e. the man, and the observed unit, i.e. his female partner, the high variability in the frequency of male intercourse, the logistical cost and ethical concerns related to the monitoring of the trial. A reasonable surrogate endpoint of the definite endpoint time to pregnancy is sperm count. In addition to the avoidance of the mentioned problems, trials that compare different treatments are possible with reasonable sample sizes, and study duration can be shorter. However, current products do not suppress sperm production to 100 per cent in all men and the sperm count is only observed with measurement error. Complete azoospermia might not be necessary in order to achieve an acceptable failure rate compared with other forms of male fertility control. Therefore, the use of sperm count as a surrogate endpoint must rely on the results of a previous trial in which both the definitive‐ and surrogate‐endpoint results were assessed. The paper discusses different estimation functions of the mean pregnancy rate (corresponding to the cumulative hazard) that are based on the results of sperm count trial and a previous trial in which both sperm count and time to pregnancy were assessed, as well as the underlying assumptions. Sample size estimations are given for pregnancy rate estimation with a given precision. Copyright © 2007 John Wiley & Sons, Ltd.
Temperature Influences the Production and Transport of Saxitoxin and the Expression of sxt Genes in the Cyanobacterium Aphanizomenon gracile

The cyanobacterium Aphanizomenon gracile is the most widely distributed producer of the potent neurotoxin saxitoxin in freshwaters. In this work, total and extracellular saxitoxin and the transcriptional response of three genes linked to saxitoxin biosynthesis (sxtA) and transport (sxtM, sxtPer) were assessed in Aphanizomenon gracile UAM529 cultures under temperatures covering its annual cycle (12 °C, 23 °C, and 30 °C). Temperature influenced saxitoxin production being maximum at high temperatures (30 °C) above the growth optimum (23 °C), concurring with a 4.3-fold increased sxtA expression at 30 °C. Extracellular saxitoxin transport was temperature-dependent, with maxima at extremes of temperature (12 °C with 16.9% extracellular saxitoxin; and especially 30 °C with 53.8%) outside the growth optimum (23 °C), coinciding with a clear upregulation of sxtM at both 12 °C and 30 °C (3.8–4.1 fold respectively), and yet with just a slight upregulation of sxtPer at 30 °C (2.1-fold). Nitrate depletion also induced a high extracellular saxitoxin release (51.2%), although without variations of sxtM and sxtPer transcription, and showing evidence of membrane damage. This is the first study analysing the transcriptional response of sxtPer under environmental gradients, as well as the effect of temperature on putative saxitoxin transporters (sxtM and sxtPer) in cyanobacteria in general.
Experiences of students in pediatric nursing clinical courses.

ISSUES AND PURPOSE Learning may be inhibited if students experience undue stress in the clinical setting. This study described the stresses, challenges, and emotions experienced by pediatric nursing students. DESIGN AND METHODS Students (n = 75) completed a modified Pagana Clinical Stress Questionnaire at the end of their pediatric nursing clinical course. The comparison group of students (n = 383) was enrolled in nonpediatric clinical courses in the same nursing programs. RESULTS The most stressful aspect of clinical practice was giving medications to children. High stress scores were related to more fear and disappointment in clinical practice. Students who experienced high stress were less stimulated by their clinical activities and developed less confidence in practice. PRACTICE IMPLICATIONS Knowledge of students' perceptions of clinical stress can help educators and clinicians promote a positive and rewarding clinical atmosphere.
An Experimental Study on the Application of Politeness Strategies Among Teachers and Students in College English Classroom

In college English classroom, teacher-student interaction has greatly influenced the acquisition of language learning. This study explores the application of Brown and Levinson’s face theory in college English classroom by analyzing the politeness strategies adopted by college English teachers and students in English as a second language (ESL) teaching based on classroom observation and MP3-recording of 10 teachers and 60 English majors for two weeks from Zhejiang Gongshang University. The findings indicate that positive and negative politeness strategies are most frequently applied in classroom teaching with the strategy of balding on-record being the least frequently strategy used in the classroom. Moreover, students are unwilling to cooperate with their teachers when they applied balding on-record strategy and are more willing to participate in the classroom activities if their teachers applied politeness strategies properly. Therefore, it is crucial that teachers apply a variety of politeness strategies in classroom to stimulate students’ learning enthusiasm and motivation.
Weak Instruments: A Guide to the Literature

Weak instruments have become an issue in many contexts in which econometric methods have been used. Some progress has been made into how one diagnoses the problem and how one makes an allowance for it. The present paper gives a partial survey of this literature, focussing upon some of the major contributions and trying to provide a relatively simple exposition of the proposed solutions.
Unprotected casual sex and perceived risk of contracting HIV among drug users in Baltimore, Maryland: evaluating the influence of non-injection versus injection drug user status

Abstract The purpose of this study was to assess the relative importance and interactive effects of drug use status (i.e. injection or non-injection drug user) and condom use with casual partners in predicting perceived risk of contracting HIV among drug users in Baltimore, Maryland. Baseline data was used from the longitudinal NEURO-HIV Epidemiological Study. This battery of questionnaires assessed a variety of demographic, drug use and sex risk variables. The current study examined these variables in association with perceived risk of contracting HIV. Significant covariates included having at least some college education (AOR=.42, 95%CI=.20, .89), knowing someone who is HIV-positive (AOR = 1.82, 95%CI = 1.15, 2.89), using drugs twice (AOR = 2.02, 95%CI = 1.02, 3.99) or more (AOR = 2.22, 95%CI = 1.22, 4.04) per day and having unprotected casual sex (AOR = 2.51, 95%CI = 1.42, 4.41). These covariates explained 15% of the variance in perceived HIV risk. A significant interaction between type of drug user and having unprotected casual sex revealed that the greatest likelihood of perceived HIV risk associated with unprotected casual sex occurred among non-injection drug users. The results suggest that non-injection drug users are aware of their risk for contracting HIV if they engage in unprotected casual sex. Future HIV-prevention programs should build on this awareness by targeting this subgroup of drug users for condom-use interventions with casual partners. Additional programs should target injection drug users to increase their perceived risk of contracting HIV through unprotected casual sex.
Using parental phenotypes in case-parent studies

In studies of case-parent triads, information is often collected about history of the condition in the parents, but typically parental phenotypes are ignored. Including that information in analyses may increase power to detect genetic association for autosomal variants. Our proposed approach uses parental phenotypes to assess association independently of the usual case-parent-based association test, enabling cross-generational internal replication for findings based on offspring and their parents. Our model for parental phenotypes also resists bias due to population stratification. We combine the information from the two generations into a single coherent model that can exploit approximate equality of parental and offspring relative risks to improve power and can also test that equality. We call the resulting procedure the Parent-phenotype Informed Likelihood Ratio Test (PPI-LRT). When some parental genotypes are missing, one can use the expectation-maximization algorithm to fit the combined model. We also develop a second composite test (PPI-CT) based on a linear combination of the parent-phenotype-based test statistic and that from the traditional log-linear, transmission-based test. We evaluate the proposed methods through non-centrality parameter calculations and simulation studies and compare them to the previously proposed approaches, parenTDT and combTDT. We show that incorporation of parental phenotype data often improves statistical power. As illustration, we apply our method to a study of young-onset breast cancer and find that it improved precision for SNPs in FGFR2 and that estimated relative risks based on triads are closely replicated using the parental data.
Proteomics‐based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies

Systemic candidiasis remains a major cause of disease and death, particularly among patients suffering from hematological malignancies. In an attempt to contribute to the discovery of useful biomarkers for its diagnosis and therapeutic monitoring, we embarked on a mapping of Candida albicans immunogenic proteins specifically recognized by antibodies produced during the natural course of systemic Candida infection in this high‐risk population. About 85 immunoreactive protein species were detected with systemic candidiasis patients' serum specimens by using immunoproteomics (i.e., two‐dimensional electrophoresis followed by Western blotting), and identified through a combination of peptide mass fingerprinting by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS), de novo peptide sequencing using nano‐electrospray ionization‐ion trap (ESI‐IT) MS, and genomic database searches. This proteomic approach has led to the characterization of 42 different housekeeping enzymes as C. albicans antigens. Their biological significance is also discussed. Furthermore, this study is the first to report that 26 of them exhibit antigenic properties in C. albicans, and 35 of them become targets of the human antibody response to systemic candidiasis. Our findings suggest that the production of antibodies to C. albicans phosphoglycerate kinase and alcohol dehydrogenase during systemic candidiasis could be associated with a differentiation of the human immune response. We also highlight the relationship between changes in maintenance of circulating levels of specific anti‐Candida antibodies and patients' outcome. Some of these variations, especially the rise of high anti‐enolase antibody concentrations, appear to be related to recovery from systemic candidiasis in these patients, which might serve as markers for predicting their outcome. This approach could therefore provide new challenges for diagnosis and clinical follow‐up of these fungal infections, and even for antifungal drug or vaccine design.
Stripe formation in the early fly embryo: principles, models, and networks

Early development of animal embryos begins from spatially distributed products of gene expression, i.e., gradients. While maternal and early zygotic genes form broad and/or terminal gradients, their direct targets appear later on as relatively narrow stripes, which foreshadow presumptive germ layers or future segments. Evidently, stripe expression of the zygotic genes is among the key mechanisms of embryo patterning. In this paper, known qualitative and quantitative models for the stripe formation are considered on the example of early embryogenesis of Drosophila. The current model analysis emphasizes the role of spatial information flow in development. Discussion is given on frequent network motifs, pointing to spatial stripe formation solutions.
The effective integration of digital games and learning content

This thesis is concerned with how the coveted user-engagement of digital games can be usefully harnessed for educational goals. Educational software has traditionally used gaming elements as a separate reward for completing learning content. The early "edutainment" sector became synonymous with this cursory "chocolate-covered broccoli" approach (Bruckman, 1999): tagging games on to learning content in order to make it more palatable. However, such methods have often proved ineffective (Kerawalla & Crook, 2005; Trushell, Burrell, & Maitland, 2001) and have been criticised for combining the worst elements of both games and education (Papert, 1998) as well as for following extrinsically motivating design models (Lepper, 1985; Parker & Lepper, 1992). This thesis provides a theoretical and empirical exploration of game designs that follow a more integrated approach. Five studies are described which detail the development and evaluation of a new theory for creating intrinsic integration based on integrating learning content with the game mechanics of a game. This includes the development of Zombie Division: a game that teaches mathematics to children through swordplay with skeletal opponents. Two experimental studies examine the motivational differences between integrated and non-integrated versions of Zombie Division by measuring time-on-task. Two more examine the educational effectiveness of integrated and non-integrated versions by measuring learning gains for a fixed amount of time-on-task. Statistically significant results are found which suggest that the integrated version is motivationally and educationally more effective than the extrinsic equivalent. Full results and implications are discussed.
A Compendium of Tests, Scales and Questionnaires: The Practitioner's Guide to Measuring Outcomes after Acquired Brain Impairment

1. Introduction Part A: Body Functions. 2. Scales of Consciousness and Orientation 3. Scales of General Cognitive Functions 4. Scales of Specific Cognitive Functions 5. Scales Assessing the Regulation of Behaviour, Thought, and Emotion 6. Scales of Sensory, Ingestion and Motor Functions. Part B: Activities and Participation 7. Scales of Activities of Daily Living 8. Scales of Participation and Social Role Part C: Contextual Factors 9. Scales of Environmental Factors Part D: Multi-Domain 10. Global and Multidimensional Scales
Clinical use of an intraoral silicoating technique.

UNLABELLED A ceramic fracture rate of metal-ceramic fixed prosthodontics of up to almost 9% calls for an efficient and effective intraoral repair system. For the repair of fractured veneering material, an intraoral silicoating technique was introduced. In contrast to other repair techniques, the silicoating can successfully be used on a variety of dental restorative materials and, therefore, offers additional applications in the field of the intraoral adhesive technique. This silicoating technique, consisting of a chairside airabrasion device filled with a specific silica-coated air-abrasion medium, has been used intraorally by the authors since 1993 for clinical purposes. The clinical procedure is described for different applications in the field of the adhesive technique: intraoral repair, preconditioning of core buildups, implant abutments, and surfaces of fixed prosthodontics for the bonding of orthodontic brackets or periodontal splints. CLINICAL SIGNIFICANCE The intraoral silicoating technique promotes reliable adhesion to the major part of metal alloy, composite, and ceramic surfaces of fixed prosthodontics. Preliminary clinical results of intraoral repairs conducted with this technique have shown that it presents a medium-term alternative to the replacement of the restoration. Also, the preliminary results of the clinical applications in other fields of adhesive dentistry are promising.
Two Novel Classes of Band-Reject Filters Realizing Broad Upper Pass Bandwidth—Synthesis and Design

The synthesis and design of two novel classes of band-reject filters capable of realizing broad upper pass bandwidth is presented in this paper. The proposed filters comprise novel coupled-line network sections whose equivalent distributed circuits are also derived in this work for the first time. By virtue of the circuit-oriented synthesis approach pursued in this study, the new filters comprise asymmetrically coupled stepped-impedance resonators. Numerical examples are presented demonstrating the step-by step synthesis and design of the two new classes of band-reject filters performing a particular electrical specification. Finally, one of the two synthesized band-reject filters is fabricated and characterized leading to a measured frequency performance exhibiting a first spurious stopband centered at five times the center frequency of the fundamental stopband.
Functional unit sharing between stacked processors in 3D integrated systems

The emerging Through Silicon Via (TSV) based 3D integration technology provides the means to stack two or more dies, enabling a low-latency interface between them. Apart of the immediate advantages of such an approach, e.g., short wires, it also opens research avenues for 3D organizations of computation platforms. In this line of reasoning we propose in this paper to share resources between stacked processors while focusing on Functional Units (FUs) inter-die sharing. The purpose of FU sharing is two fold: (i) it enables inexpensive fault tolerance by allowing, when possible, redundant instruction execution on idle FUs of processors located on other stack dies; and (ii) it can result in performance improvements by remotely executing instructions on idle FUs located on other dies in the 3D stack, when more instructions than locally available FUs are issuable. We evaluated the potential implications of our proposal on a 3D system built with two stacked processors (dies). In this case only a limited error detection capability is enabled and the experimental results indicate that our scheme covers on average 46% of the executed instructions. When performance improvement is targeted an average speedup of 6.9% can be achieved for the applications running on the considered two die stack.
Continuous Assessment of Presence in Stereoscopic Displays

Presence, a sense of ‘being there’ evoked by a display, can be regarded as a concept of central importance in the evaluation of broadcasting and entertainment services in general and virtual reality applications in particular. Subjective methods of assessing presence that have either been used or proposed to date do not provide a measure of temporal variation in observers' presence. To overcome this limitation, we have applied the method of continuous assessment (ITU-R, BT 500-7) to the measurement of presence. Thirty observers (twelve at IPO, eighteen at UoE) with normal or corrected-to-normal vision and good stereo-acuity viewed a stereoscopic film. While watching, observers were asked to continuously rate their perceptions of depth, naturalness and presence. The stimulus material varied considerably in the amount and strength of the visual cues presented over time. This enabled us to investigate whether the extent of sensory information presented to an observer was a determinant of presence, as proposed by Sheridan [1992 Presence: Teleoperators and Virtual Environments 1(1) 120 – 125]. The results, which were very similar across two independent laboratories, suggested that continuous assessment provides a promising methodology for the subjective assessment of temporal variation in the observer's sense of presence. Further, increasing the extent of sensory information presented to an observer may enhance the sense of presence, provided the depth cues introduced are consistent and within natural bounds. [Note: First and second author in arbitrary order. ]
Comparison of platforms for high frequency data processing

The aim of this paper is to find and compare existing solutions of complex event processing platforms (CEP). We intend to use CEP platform for prediction of complex time series and integrate a solution for newly proposed method of decision making. As there are lots of solutions we will take the following characteristics under consideration - the processing in real time, possibility of processing of high volume data from multiple sources, platform independence, platform allowing integration with user solution. At first we will talk about existing CEP tools and their specific way of use in praxis. Then we will mention the design of method for formalization of business rules used for decision making. Afterwards, we focus on two platforms which seem to be the best fit for integration of our solution and we will list the main pros and cons of each approach. Final part is devoted to benchmark platforms for CEP.
Towards a Brain-Sensitive Intelligent Tutoring System: Detecting Emotions from Brainwaves

This paper proposes and evaluates a multiagents system called NORA that predicts emotional attributes from learners' brainwaves within an intelligent tutoring system. The measurements from the electrical brain activity of the learner are combined with information about the learner's emotional attributes. Electroencephalogram was used to measure brainwaves and self-reports to measure the three emotional dimensions: pleasure, arousal, and dominance, the eight emotions occurring during learning: anger, boredom, confusion, contempt curious, disgust, eureka, and frustration, and the emotional valence positive for learning and negative for learning. The systemis evaluated on natural data, and it achieves an accuracy of over 63%, significantly outperforming classification using the individual modalities and several other combination schemes.
Neighbor Joining Algorithms for Inferring Phylogenies via LCA Distances

Reconstructing phylogenetic trees efficiently and accurately from distance estimates is an ongoing challenge in computational biology from both practical and theoretical considerations. We study algorithms which are based on a characterization of edge-weighted trees by distances to LCAs (Least Common Ancestors). This characterization enables a direct application of ultrametric reconstruction techniques to trees which are not necessarily ultrametric. A simple and natural neighbor joining criterion based on this observation is used to provide a family of efficient neighbor-joining algorithms. These algorithms are shown to reconstruct a refinement of the Buneman tree, which implies optimal robustness to noise under criteria defined by Atteson. In this sense, they outperform many popular algorithms such as Saitou and Nei's NJ. One member of this family is used to provide a new simple version of the 3-approximation algorithm for the closest additive metric under the iota (infinity) norm. A byproduct of our work is a novel technique which yields a time optimal O (n (2)) implementation of common clustering algorithms such as UPGMA.