Miracle-dz/UniFAR-FTUs huggingface dataset:
A genetic assessment of polyandry and breeding‐site fidelity in lemon sharks

We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding‐site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life‐history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.
Mitochondrial function in human skeletal muscle following high‐altitude exposure

• What is the central question of this study? Are the enzymatic alterations in human skeletal muscle observed following 9–11 days of exposure to high altitude reflected in mitochondrial function? • What is the main finding and its importance? The main findings of this study are that the capacity fat oxidation, individualized respiration capacity through mitochondrial complex I and II, and electron coupling efficiency are not greatly affected by 9–11 days of exposure to high altitude. The importance of this data is that high altitude exposure failed to affect integrated measures of mitochondrial functional capacity in skeletal muscle despite significant decrements to enzyme concentrations involved in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation.
Carotid Baroreceptors in Fetal and Newborn Sheep

ABSTRACT: The responses of single carotid baroreceptor afferents were determined in anaesthetized fetal lambs at 88–113 and 131–144 days gestation, and in newborn lambs 1–8 and 30–40 days old. The baroreceptors discharged in synchrony with the arterial pressure pulse and increased their discharge rate as pressure was raised by compression of the abdominal aorta. When step increases in pressure were applied to the vascularly isolated carotid sinus, baroreceptor discharge increased abruptly and then showed adaptation to a steady state level. Basal mean arterial pressure increased from 49.1 in the young fetuses to 87.5 mm Hg in the 30− to 40-day-old lambs without an accompanying increase in ban] baroreceptor discharge expressed absolutely or as a function of maximum discharge for each unit. The slope of the steep portion of the stimulus-response curve decreased with gestational age from 7.89 ± 1.57 (mean ± SE) at 88–113 days gestation to 1.82 ± 0.37% nerve activity-min Hg-1 in the 30− to 49-day-old lambs. Dynamic and steady state response curves were determined using step increases in carotid sinus pressure in two fetal lambs of 135 days gestation and two lambs 8 days old. Both the dynamic and the steady state curves were less steep in the older lambs. We conclude that the sensitivity of the carotid baroreceptors is reset as arterial pressure increases throughout the last third of gestation and the first postnatal month. This resetting is seen as a shift to the right of the response curve and a decrease in its slope. Our results suggest that the afferent limb of the baroreflex can be elicited throughout this period, but that its sensitivity decreases with age.
VOICE ONSET TIME AND THE SCOTTISH VOWEL LENGTH RULE IN ABERDEEN ENGLISH

Voice Onset Time (VOT) was measured in wordinitial /p t k b d / produced by 9 speakers of Aberdeen English (AE). The durations of /i e  a  o u/ and /ai/ were also measured to assess the extent to which the Scottish Vowel Length Rule (SVLR) [2] operates in the Aberdeen vowel system.
Non-Invasive MRI and Spectroscopy of mdx Mice Reveal Temporal Changes in Dystrophic Muscle Imaging and in Energy Deficits

In Duchenne muscular dystrophy (DMD), a genetic disruption of dystrophin protein expression results in repeated muscle injury and chronic inflammation. Magnetic resonance imaging shows promise as a surrogate outcome measure in both DMD and rehabilitation medicine that is capable of predicting clinical benefit years in advance of functional outcome measures. The mdx mouse reproduces the dystrophin deficiency that causes DMD and is routinely used for preclinical drug testing. There is a need to develop sensitive, non-invasive outcome measures in the mdx model that can be readily translatable to human clinical trials. Here we report the use of magnetic resonance imaging and spectroscopy techniques for the non-invasive monitoring of muscle damage in mdx mice. Using these techniques, we studied dystrophic mdx muscle in mice from 6 to 12 weeks of age, examining both the peak disease phase and natural recovery phase of the mdx disease course. T2 and fat-suppressed imaging revealed significant levels of tissue with elevated signal intensity in mdx hindlimb muscles at all ages; spectroscopy revealed a significant deficiency of energy metabolites in 6-week-old mdx mice. As the mdx mice progressed from the peak disease stage to the recovery stage of disease, each of these phenotypes was either eliminated or reduced, and the cross-sectional area of the mdx muscle was significantly increased when compared to that of wild-type mice. Histology indicates that hyper-intense MRI foci correspond to areas of dystrophic lesions containing inflammation as well as regenerating, degenerating and hypertrophied myofibers. Statistical sample size calculations provide several robust measures with the ability to detect intervention effects using small numbers of animals. These data establish a framework for further imaging or preclinical studies, and they support the development of MRI as a sensitive, non-invasive outcome measure for muscular dystrophy.
Scorpion: Explaining Away Outliers in Aggregate Queries

Database users commonly explore large data sets by running aggregate queries that project the data down to a smaller number of points and dimensions, and visualizing the results. Often, such visualizations will reveal outliers that correspond to errors or surprising features of the input data set. Unfortunately, databases and visualization systems do not provide a way to work backwards from an outlier point to the common properties of the (possibly many) unaggregated input tuples that correspond to that outlier. We propose Scorpion, a system that takes a set of user-specified outlier points in an aggregate query result as input and finds predicates that explain the outliers in terms of properties of the input tuples that are used to compute the selected outlier results. Specifically, this explanation identifies predicates that, when applied to the input data, cause the outliers to disappear from the output. To find such predicates, we develop a notion of influence of a predicate on a given output, and design several algorithms that efficiently search for maximum influence predicates over the input data. We show that these algorithms can quickly find outliers in two real data sets (from a sensor deployment and a campaign finance data set), and run orders of magnitude faster than a naive search algorithm while providing comparable quality on a synthetic data set.
Anaesthesia for Caesarean section and neonatal acid‐base status: a meta‐analysis *

Spinal anaesthesia is generally preferred for Caesarean section. Its superiority for the baby is often assumed. Umbilical artery acid‐base status provides a valid index of fetal welfare. Twenty‐seven studies reporting neonatal acid‐base data with different types of anaesthesia were used to compare umbilical artery or vein pH and base deficit, using random‐effect meta‐analysis. Cord pH was significantly lower with spinal than with both general (difference: −0.015; 95% CI −0.029 to −0.001; 13 studies, 1272 subjects) and epidural anaesthesia (difference −0.013; 95% CI −0.024 to −0.002; 11 studies, 828 subjects). Larger doses of ephedrine contributed to the latter effect (p = 0.023). Sixteen studies reported a base deficit, which was significantly higher for spinal than for general (difference 1.109; 95% CI 0.434–1.784 mEq.l−1; seven studies, 695 subject) and epidural anaesthesia (difference 0.910; 95% CI 0.222–1.598 mEq.l−1; seven studies, 497 subjects). Spinal anaesthesia cannot be considered safer than epidural or general anaesthesia for the fetus.
A Scalable Approach to Size-Independent Network Similarity

Given a set of k networks, possibly with different sizes and no overlaps in nodes or edges, how can we quickly assess similarity between them, without solving the node-correspondence problem? Analogously, how can we extract a small number of descriptive, numerical features from each graph that effectively serve as the graph’s “signature”? Having such features will enable a wealth of graph mining tasks, including clustering, outlier detection, visualization, etc. We propose NETSIMILE – a novel, effective, and scalable method for solving the aforementioned problem. NETSIMILE has the following desirable properties: (a) It gives similarity scores that are size-invariant. (b) It is scalable, being linear on the number of edges for “signature” vector extraction. (c) It does not need to solve the node-correspondence problem. We present extensive experiments on numerous synthetic and real graphs from disparate domains, and show NETSIMILE’s superiority over baseline competitors. We also show how NETSIMILE enables several mining tasks such as clustering, visualization, and discontinuity detection.
Unimpaired Attentional Disengagement and Social Orienting in Children With Autism

Visual attention is often hypothesized to play a causal role in the development of autism spectrum disorder (ASD). Because attention shapes perception, learning, and social interaction, early deficits in attention could substantially affect the development of other perceptual and cognitive abilities. Here we test two key attentional phenomena thought to be disrupted in autism: attentional disengagement and social orienting. We find in a free-viewing paradigm that both phenomena are present in high-functioning children with ASD (n = 44, ages 5–12 years) and are identical in magnitude to those in age- and IQ-matched typical children (n = 40). Although these attentional processes may malfunction in other circumstances, our data indicate that high-functioning children with ASD do not suffer from across-the-board disruptions of either attentional disengagement or social orienting. Combined with mounting evidence that other attentional abilities are largely intact, it seems increasingly unlikely that disruptions of core attentional abilities lie at the root of ASD.
Numerical algorithm for solving cross-coupled algebraic Riccati equations related to Nash games of multimodeling systems

In this paper, the numerical design of a Nash equilibrium for infinite horizon multiparameter singularly perturbed systems (MSPS) is analyzed. A new algorithm which is based on the Newton method for solving the generalized cross-coupled multiparameter algebraic Riccati equations (GCMARE), is proposed. It is proven that the proposed algorithm guarantees the quadratic convergence. As a result, it is shown the proposed algorithm succeed in improving the convergence rate dramatically compared with the existing results.
Internet Advocacy Support for Families of Children with Emotional Difficulties.

This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact ecommons@luc.edu. Julia and Reese so they may understand the importance and joy of lifelong learning and that hard work and perseverance can bring your dreams to fruition. To my husband, Bill who has supported every aspiration of mine throughout our many years together with love and understanding and when necessary, humor. Thank you. To our children: John been the greatest accomplishment of my life and I thank you for the help and support you have given me. I must especially thank Bridget whose endless willingness to help gave me valuable time to work and Joe whose statistical tutelage was an important component of my ability to complete this undertaking. To all of my family and friends especially Deb, with whom I am celebrating 50 years as best friends, and my sister-in-law, Kathy your encouragement and support meant so much. To the memory of my Mom and Dad, Irene, Tim, Rich, Sue, Marge and my sister Mary (Noonie) who all would have been so proud to see me finish my doctorate. My appreciation to the entire Loyola University community for their help and understanding throughout my journey to completion, particularly Dr. Pamela Fenning and Dr. Patricia Mooney-Melvin who understood the issues pertinent to the non-traditional student and provided endless assistance and support. iv My never-ending gratitude to my committee, Dr. for their time, patience, and valuable input. To Valerie Collier, whose friendship, support and computer skills will long be remembered. Finally, the endless efforts of Dr. Martha Ellen Wynne, my director, my advisor and my advocate, must be noted. Your mentorship and friendship is a gift that I will treasure always. It has been an honor and privilege filled with memories that I will carry with me forever. Thank you.
Hierarchies of Models: Toward Understanding Planetary Nebulae

Stars like our sun (initial masses between 0.8 to 8 solar masses) end their lives as swollen red giants surrounded by cool extended atmospheres. The nuclear reactions in their cores create carbon, nitrogen and oxygen, which are transported by convection to the outer envelope of the stellar atmosphere. As the star finally collapses to become a white dwarf, this envelope is expelled from the star to form a planetary nebula (PN) rich in organic molecules. The physics, dynamics, and chemistry of these nebulae are poorly understood and have implications not only for our understanding of the stellar life cycle but also for organic astrochemistry and the creation of prebiotic molecules in interstellar space. We are working toward generating three‐dimensional models of planetary nebulae (PNe), which include the size, orientation, shape, expansion rate and mass distribution of the nebula. Such a reconstruction of a PN is a challenging problem for several reasons. First, the data consist of images obtained over tim.
Hypertensive disorders of pregnancy in women with Type 1 and Type 2 diabetes

Aims Hypertensive disorders in pregnancy are common in women with Type 1 diabetes and can be associated with adverse fetal outcomes, but little is known about hypertension in pregnancy in women with Type 2 diabetes. The aim of this study was to compare the incidence and outcomes of, and risk factors for, hypertension in pregnancy in women with Type 1 and Type 2 diabetes.
NICE guidance: a comparative study of the introduction of the single technology appraisal process and comparison with guidance from Scottish Medicines Consortium

Objectives To compare the timelines and recommendations of the Scottish Medicines Consortium (SMC) and National Institute of Health and Clinical Excellence (NICE), in particular since the single technology assessment (STA) process was introduced in 2005. Design Comparative study of drug appraisals published by NICE and SMC. Setting NICE and SMC. Participants All drugs appraised by SMC and NICE, from establishment of each organisation until August 2010, were included. Data were gathered from published reports on the NICE website, SMC annual reports and European Medicines Agency website. Primary and secondary outcome measures Primary outcome was time from marketing authorisation until publication of first guidance. The final outcome for each drug was documented. Drug appraisals by NICE (before and after the introduction of the STA process) and SMC were compared. Results NICE and SMC appraised 140 drugs, 415 were appraised by SMC alone and 102 by NICE alone. NICE recommended, with or without restriction, 90% of drugs and SMC 80%. SMC published guidance more quickly than NICE (median 7.4 compared with 21.4 months). Overall, the STA process reduced the average time to publication compared with multiple technology assessments (median 16.1 compared with 22.8 months). However, for cancer medications, the STA process took longer than multiple technology assessment (25.2 compared with 20.0 months). Conclusions Proportions of drugs recommended for NHS use by SMC and NICE are similar. SMC publishes guidance more quickly than NICE. The STA process has improved the time to publication but not for cancer drugs. The lengthier time for NICE guidance is partly due to measures to provide transparency and the widespread consultation during the NICE process.
Risk factors for incident HIV infection among antenatal mothers in rural Eastern Cape, South Africa

Background The prevalence of HIV among antenatal clients in South Africa has remained at a very high rate of about 29% despite substantial decline in several sub-Saharan countries. There is a paucity of data on risk factors for incident HIV infection among antenatal mothers and women within the reproductive age bracket in local settings in the Eastern Cape, South Africa. Objective To establish the risk factors for incident HIV infection among antenatal clients aged 18–49 years attending public antenatal clinics in rural Eastern Cape, South Africa. Design This was an unmatched case–control study carried out in public health antenatal clinics of King Sabata District Municipality between January and March 2014. The cases comprised 100 clients with recent HIV infection; the controls were 200 HIV-negative antenatal clients. Socio-demographic, sexual, and behavioral data were collected using interviewer-administered questionnaires adapted from the standard DHS5 women's questionnaire. Multivariate logistic regression models were used to identify the independent risk factors for HIV infection. A p<0.05 was considered statistically significant. Results The independent risk factors for incident HIV infection were economic dependence on the partner, having older male partners especially among women aged ≤20 years, and sex under the influence of alcohol. Conclusions Therefore, effective prevention of HIV among antenatal mothers in KSDM must target the improvement of the economic status of women, thereby reducing economic dependence on their sexual partners; address the prevalent phenomenon of cross-generation sex among women aged <20 years; and regulate the brewing, marketing, and consumption of alcohol.
Puma response to the effects of fire and urbanization

In southern California, wildfire and urbanization influence landscape condition and features. We explored the synergistic effects of these disturbances on puma (Puma concolor) movement and habitat preference in southern California, USA using a telemetry dataset of >40 individuals from 2001 to 2011. We examined post-fire movement of tracked pumas to consider the relationship between habitat use and availability as animals used the landscape. We also explored puma response to burned areas to examine the influence of vegetation cover, time since fire, fire frequency, and the synergistic effects of urbanization on puma landscape use. We compare our results to those of others by using a complementary approach to evaluate how habitat relationships change with additional puma data and with consideration of the fire history of the landscape. Our analyses suggest that after fires, pumas use burned habitats opportunistically, responding to post-fire changes in prey density. Additionally, time since fire and fire frequency were useful predictors of puma presence at the individual- and population-level. Our puma habitat models showed a strong relationship between puma habitat use, vegetation, and human developments. Our analysis suggests that fire is an important landscape element to consider when evaluating puma habitat; pumas opportunistically used recently burned areas in the first few years after fire. We identified that pumas avoided grassland vegetation types and areas of sparse cover, suggesting that increasing fire frequency could affect puma habitat suitability and connectivity in the future. Fire frequencies in parts of southern California have already increased beyond the threshold to which the ecosystem is resilient, and if this trend continues across the region, suitable puma habitat may be lost through vegetation-type conversion to homogenous non-native annual grasslands, a habitat avoided by pumas during foraging and resting. We suggest monitoring responses to increasing fire frequency to assess how pumas and other carnivores will be affected by large-scale changes that may pose a threat to landscape integrity and persistence of puma populations in southern California. © 2015 The Wildlife Society.
The Geometry of Scheduling

We consider the following general scheduling problem: The input consists of $n$ jobs, each with an arbitrary release time, size, and a monotone function specifying the cost incurred when the job is completed at a particular time. The objective is to find a preemptive schedule of minimum aggregate cost. This problem formulation is general enough to include many natural scheduling objectives, such as weighted flow, weighted tardiness, and sum of flow squared. The main contribution of this paper is a randomized polynomial-time algorithm with an approximation ratio $O(\log \log nP )$, where $P$ is the maximum job size. We also give an $O(1)$ approximation in the special case when all jobs have identical release times. Initially, we show how to reduce this scheduling problem to a particular geometric set-cover problem. We then consider a natural linear programming formulation of this geometric set-cover problem, strengthened by adding knapsack cover inequalities, and show that rounding the solution of this linear program can be reduced to other particular geometric set-cover problems. We then develop algorithms for these sub-problems using the local ratio technique, and Varadarajan's quasi-uniform sampling technique. This general algorithmic approach improves the best known approximation ratios by at least an exponential factor (and much more in some cases) for essentially all of the nontrivial common special cases of this problem. We believe that this geometric interpretation of scheduling is of independent interest.
Crystal structure of recombinant triosephosphate isomerase from bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three‐dimensional structures points to the importance of hydrophobic interactions

The structure of the thermostable triosephosphate isomerase (TIM) from Bacillus stearothermophilus complexed with the competitive inhibitor 2‐phosphoglycolate was determined by X‐ray crystallography to a resolution of 2.8 A. The structure was solved by molecular replacement using XPLOR. Twofold averaging and solvent flattening was applied to improve the quality of the map. Active sites in both the subunits are occupied by the inhibitor and the flexible loop adopts the “closed” conformation in either subunit. The crystallographic R‐factor is 17.6% with good geometry. The two subunits have an RMS deviation of 0.29 Å for 248 Cα atoms and have average temperature factors of 18.9 and 15.9 A2, respectively. In both subunits, the active site Lys 10 adopts an unusual ϕ,ψ combination.