Miracle-dz/UniFAR-FTUs huggingface dataset:
Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.
Influence of a Locomotor Training Approach on Walking Speed and Distance in People With Chronic Spinal Cord Injury: A Randomized Clinical Trial

Background Impaired walking limits function after spinal cord injury (SCI), but training-related improvements are possible even in people with chronic motor incomplete SCI. Objective The objective of this study was to compare changes in walking speed and distance associated with 4 locomotor training approaches. Design This study was a single-blind, randomized clinical trial. Setting This study was conducted in a rehabilitation research laboratory. Participants Participants were people with minimal walking function due to chronic SCI. Intervention Participants (n=74) trained 5 days per week for 12 weeks with the following approaches: treadmill-based training with manual assistance (TM), treadmill-based training with stimulation (TS), overground training with stimulation (OG), and treadmill-based training with robotic assistance (LR). Measurements Overground walking speed and distance were the primary outcome measures. Results In participants who completed the training (n=64), there were overall effects for speed (effect size index [d]=0.33) and distance (d=0.35). For speed, there were no significant between-group differences; however, distance gains were greatest with OG. Effect sizes for speed and distance were largest with OG (d=0.43 and d=0.40, respectively). Effect sizes for speed were the same for TM and TS (d=0.28); there was no effect for LR. The effect size for distance was greater with TS (d=0.16) than with TM or LR, for which there was no effect. Ten participants who improved with training were retested at least 6 months after training; walking speed at this time was slower than that at the conclusion of training but remained faster than before training. Limitations It is unknown whether the training dosage and the emphasis on training speed were optimal. Robotic training that requires active participation would likely yield different results. Conclusions In people with chronic motor incomplete SCI, walking speed improved with both overground training and treadmill-based training; however, walking distance improved to a greater extent with overground training.
NORA/HAMMR: making deduction-based software component retrieval practical

Deduction-based software component retrieval uses pre- and postconditions as indexes and search keys and an automated theorem prover (ATP) to check whether a component matches. This idea is very simple but the vast number of arising proof tasks makes a practical implementation very hard. We thus pass the components through a chain of filters of increasing deductive power. In this chain, rejection filters based on signature matching and model checking techniques are used to rule out non-matches as early as possible and to prevent the subsequent ATP from "drowning". Hence, intermediate results of reasonable precision are available at (almost) any time of the retrieval process. The final ATP step then works as a confirmation filter to lift the precision of the answer set. We implemented a chain which runs fully automatically and uses SETHEO for model checking and the automated prover SETHEO as confirmation filter. We evaluated the system over a medium-sized collection of components. The results encourage our approach.
Looking Ahead: Anticipatory Gaze and Motor Ability in Infancy

The present study asks when infants are able to selectively anticipate the goals of observed actions, and how this ability relates to infants’ own abilities to produce those specific actions. Using eye-tracking technology to measure on-line anticipation, 6-, 8- and 10-month-old infants and a control group of adults were tested while observing an adult reach with a whole hand grasp, a precision grasp or a closed fist towards one of two different sized objects. The same infants were also given a comparable action production task. All infants showed proactive gaze to the whole hand grasps, with increased degrees of proactivity in the older groups. Gaze proactivity to the precision grasps, however, was present from 8 months of age. Moreover, the infants’ ability in performing precision grasping strongly predicted their ability in using the actor’s hand shape cues to differentially anticipate the goal of the observed action, even when age was partialled out. The results are discussed in terms of the specificity of action anticipation, and the fine-grained relationship between action production and action perception.
The clock gene, brain and muscle Arnt‐like 1, regulates adipogenesis via Wnt signaling pathway

Circadian clocks in adipose tissue are known to regulate adipocyte biology. Although circadian dysregulation is associated with development of obesity, the underlying mechanism has not been established. Here we report that disruption of the clock gene, brain and muscle Arnt‐like 1 (Bmal1), in mice led to increased adipogenesis, adipocyte hypertrophy, and obesity, compared to wild‐type (WT) mice. This is due to its cell‐autonomous effect, as Bmal1 deficiency in embryonic fibroblasts, as well as stable shRNA knockdown (KD) in 3T3‐L1 preadipocyte and C3H10T1/2 mesenchymal stem cells, promoted adipogenic differentiation. We demonstrate that attenuation of Bmal1 function resulted in down‐regulation of genes in the canonical Wnt pathway, known to suppress adipogenesis. Promoters of these genes (Wnt10a, β‐catenin, Dishevelled2, TCF3) displayed Bmal1 occupancy, indicating direct circadian regulation by Bmal1. As a result, Wnt signaling activity was attenuated by Bmal1 KD and augmented by its overexpression. Furthermore, stabilizing β‐catenin through Wnt ligand or GSK‐3β inhibition achieved partial restoration of blunted Wnt activity and suppression of increased adipogenesis induced by Bmal1 KD. Taken together, our study demonstrates that Bmal1 is a critical negative regulator of adipocyte development through transcriptional control of components of the canonical Wnt signaling cascade, and provides a mechanistic link between circadian disruption and obesity. —Guo, B. , Chatterjee, S. , Li, L. , Kim, J. M. , Lee, J., Yechoor, V. K. , Minze, L. J., Hsueh, W. , Ma, K. The clock gene, brain and muscle Arnt‐like 1, regulates adipogenesis via Wnt signaling pathway. FASEB J. 26, 3453–3463 (2012). www.fasebj. org
Mechanisms of drug resistance: daptomycin resistance

Daptomycin (DAP) is a cyclic lipopeptide with in vitro activity against a variety of Gram‐positive pathogens, including multidrug‐resistant organisms. Since its introduction into clinical practice in 2003, DAP has become an important key frontline antibiotic for severe or deep‐seated infections caused by Gram‐positive organisms. Unfortunately, DAP resistance (DAP‐R) has been extensively documented in clinically important organisms such as Staphylococcus aureus, Enterococcus spp. , and Streptococcus spp. Studies on the mechanisms of DAP‐R in Bacillus subtilis and other Gram‐positive bacteria indicate that the genetic pathways of DAP‐R are diverse and complex. However, a common phenomenon emerging from these mechanistic studies is that DAP‐R is associated with important adaptive changes in cell wall and cell membrane homeostasis with critical changes in cell physiology. Findings related to these adaptive changes have provided novel insights into the genetics and molecular mechanisms of bacterial cell envelope stress response and the manner in which Gram‐positive bacteria cope with the antimicrobial peptide attack and protect vital structures of the cell envelope, such as the cell membrane. In this review, we will examine the most recent findings related to the molecular mechanisms of resistance to DAP in relevant Gram‐positive pathogens and discuss the clinical implications for therapy against these important bacteria.
Adipokinetic hormone signaling through the gonadotropin-releasing hormone receptor modulates egg-laying in Caenorhabditis elegans

In mammals, hypothalamic gonadotropin-releasing hormone (GnRH) is a neuropeptide that stimulates the release of gonadotropins from the anterior pituitary. The existence of a putative functional equivalent of this reproduction axis in protostomian invertebrates has been a matter of debate. In this study, the ligand for the GnRH receptor in the nematode Caenorhabditis elegans (Ce-GnRHR) was found using a bioinformatics approach. The peptide and its precursor are reminiscent of both insect adipokinetic hormones and GnRH-preprohormone precursors from tunicates and higher vertebrates. We cloned the AKH-GnRH-like preprohormone and the Ce-GnRHR and expressed the GPCR in HEK293T cells. The GnRHR was activated by the C. elegans AKH-GnRH-like peptide (EC50 = 150 nM) and by Drosophila AKH and other nematode AKH-GnRHs that we found in EST databases. Analogous to both insect AKH receptor and vertebrate GnRH receptor signaling, Ce-AKH-GnRH activated its receptor through a Gαq protein with Ca2+ as a second messenger. Gene silencing of Ce-GnRHR, Ce-AKH-GnRH, or both resulted in a delay in the egg-laying process, comparable to a delay in puberty in mammals lacking a normal dose of GnRH peptide or with a mutated GnRH precursor or receptor gene. The present data support the view that the AKH-GnRH signaling system probably arose very early in metazoan evolution and that its role in reproduction might have been developed before the divergence of protostomians and deuterostomians.
Multiple-Choice Tests and Student Understanding: What Is the Connection?

Instructors can use both “multiple-choice” (MC) and “constructed response” (CR) questions (such as short answer, essay, or problem-solving questions) to evaluate student understanding of course materials and principles. This article begins by discussing the advantages and concerns of using these alternate test formats and reviews the studies conducted to test the hypothesis (or perhaps better described as the hope) that MC tests, by themselves, perform an adequate job of evaluating student understanding of course materials. Despite research from educational psychology demonstrating the potential for MC tests to measure the same levels of student mastery as CR tests, recent studies in specific educational domains find imperfect relationships between these two performance measures. We suggest that a significant confound in prior experiments has been the treatment of MC questions as homogeneous entities when in fact MC questions may test widely varying levels of student understanding. The primary contribution of the article is a modified research model for CR/MC research based on knowledge-level analyses of MC test banks and CR question sets from basic computer language programming. The analyses are based on an operationalization of Bloom's Taxonomy of Learning Goals for the domain, which is used to develop a skills-focused taxonomy of MC questions. However, we propose that their analyses readily generalize to similar teaching domains of interest to decision sciences educators such as modeling and simulation programming.
Robust Interaction Control of a Dielectric Elastomer Actuator With Variable Stiffness

This paper presents an interaction control algorithm for a dielectric elastomer membrane actuator. The proposed method permits efficient exploitation of the controllable stiffness of the material, allowing to use the membrane as a “programmable spring” in applications such as robotic manipulation or haptic devices. To achieve this goal, we propose a design algorithm based on robust control theory and linear matrix inequalities. The resulting controller permits to arbitrarily shape the stiffness of the elastomer, while providing robust stability and performance with respect to model nonlinearities. A self-sensing displacement estimation algorithm allows implementation of the method without the need of a deformation sensor, thus reducing cost and size of the system. The approach is validated on an experimental prototype consisting of an elastomer membrane preloaded with a bistable biasing spring.
Prospective Randomized Comparison of Oral Sodium Phosphate and Sennoside A+B Calcium Lavage for Colonoscopy Preparation

Purpose The aim of this study is to assess 2 different bowel-cleansing agents. Methods The patients were prospectively randomized to 2 arms of sodium phosphate versus Sennoside A+B calcium preparation. Laboratory assessment, body weight, height, and vital signs were obtained at baseline and before colonoscopy. A self-administered questionnaire was completed by the patients. The time taken to complete the colonoscopy and the segment of the colon examined were recorded. Results The patients in the Sennoside A+B calcium group were more comfortable with the taste of the solution. Patients using sodium phosphate faced more nausea and significantly lower Ca levels and P values. The pulse rate was significantly higher in this group. Patients in the sennoside group had better grades of bowel cleansing in sigmoid and descending segments of the colon. Conclusions Sennoside A+B calcium is more effective in some of the colonic segmental cleansing, causes fewer changes on serum electrolyte levels, and is better tolerated.
Molecular Epidemiology of Clinical Cryptococcus neoformans Strains from India

ABSTRACT Little is known about the molecular epidemiology of the human pathogenic fungus Cryptococcus neoformans in India, a country now in the midst of an epidemic of AIDS-related cryptococcosis. We studied 57 clinical isolates from several regions in India, of which 51 were C. neoformans var. grubii, 1 was C. neoformans var. neoformans, and 5 were C. neoformans var. gattii. This strain set included 18 additional sequential isolates from 14 patients. Strains were characterized phenotypically by measuring the polysaccharide capsule and by determining the MICs of standard antifungals. Molecular typing was performed by a PCR-based method using the minisatellite-specific core sequence (M13), by electrophoretic karyotyping, by restriction fragment length polymorphisms with the C. neoformans transposon 1 (TCN-1), and by URA5 DNA sequence analysis. Overall, Indian isolates were less heterogeneous than isolates from other regions and included a subset that clustered into one group based on URA5 DNA sequence analysis. In summary, our results demonstrate (i) differences in genetic diversity of C. neoformans isolates from India compared to isolates from other regions in the world; (ii) that DNA typing with the TCN-1 probe can adequately distinguish C. neoformans var. grubii strains; (iii) that TCN-1 sequences are absent in many C. neoformans var. gattii strains, supporting previous studies indicating that these strains have a limited geographical dispersal; and (iv) that human cryptococcal infection can be associated with microevolution of the infecting strain and by simultaneous coinfection with two distinct C. neoformans strains.
A Preliminary Outcome Study of a Community Group Treatment Programme for Emotionally Disturbed Adolescents

The treatment of adolescents with psychiatric disturbance remains a highly unsuccessful area. Empirical research is limited and treatment decisions are often based on theoretical bias rather than proven results. This study reports on the results of a multivariate analysis of pre- and post-individual and family measures on patients in a community based day and evening programme. The programme utilized a broad range of treatment modalities including group and family therapy and chemotherapy. An accredited educational programme was also provided to the patients attending the day programme. The results of this study showed that adolescents were referred to either the day or evening programme components based on level of acting out behaviour rather than on DSM III diagnosis. Adolescents reported significant positive changes at post testing in all areas, but this improvement was not endorsed by parents. Although therapists perceived considerable improvement in their families after treatment, this improvement did not show up on the family assessment measure chosen. The findings of the study endorse the need for further empirical research in adolescent treatment and underscores the fallacy of relying on anecdotal evidence to report treatment results. Questions are raised as to the operational usefulness of the present DSM III criteria in making treatment decisions and the validity of associating individual dysfunction with family dysfunction. Some question as to the sensitivity of the family measure used was also raised. The study outlined strengths and weaknesses in the present treatment programme and underscored the importance of further evaluative research, if the treatment of adolescents with psychiatric disturbance is to become successful.
Fusing Multiple Two Frame Depth Estimates for 3D Reconstruction with Unknown Noise Distribution

The problem of structure from motion (SFM) is to extract the three-dimensional model of a moving scene from a sequence of images. Traditional SFM algorithms use just two images but produce inaccurate reconstructions of the 3D scene because of incorrect estimation of the motion. Recently, algorithms have been proposed that use multiple (> 2) frames. This paper proposes a computationally e(cid:14)cient framework for estimating structure from an image sequence taking into consideration the error in the 2-frame estimates, but without recourse to strong statistical assumptions on the observations. We propose a simple way to model the observations, which are the depth estimates obtained from traditional 2-frame SFM algorithms, and present a batch and a recursive solu-tion to the multiframe estimation process. Our algorithms use bootstrapping and stochastic approximation methods. We also propose a method to estimate the number of frames to be used in the recursive so-lution using the Fisher information criterion. The algorithms were primarily applied to model human face and a number of experimental results are reported.
Macrophysiology: A Conceptual Reunification

Widespread recognition of the importance of biological studies at large spatial and temporal scales, particularly in the face of many of the most pressing issues facing humanity, has fueled the argument that there is a need to reinvigorate such studies in physiological ecology through the establishment of a macrophysiology. Following a period when the fields of ecology and physiological ecology had been regarded as largely synonymous, studies of this kind were relatively commonplace in the first half of the twentieth century. However, such large‐scale work subsequently became rather scarce as physiological studies concentrated on the biochemical and molecular mechanisms underlying the capacities and tolerances of species. In some sense, macrophysiology is thus an attempt at a conceptual reunification. In this article, we provide a conceptual framework for the continued development of macrophysiology. We subdivide this framework into three major components: the establishment of macrophysiological patterns, determining the form of those patterns (the very general ways in which they are shaped), and understanding the mechanisms that give rise to them. We suggest ways in which each of these components could be developed usefully.
Multi-agent architecture for reliable Cyber-Physical Systems (CPS)

High reliability is an important characteristic of Cyber-Physical Systems (CPS). New CPS components/subsystems have to be developed for the detection, isolation, recovery and prevention of failures and external attacks. To address this challenge, we propose a multi-agent-based subsystem architecture that can detect and prevent CPS hardware components' failures. The architecture comprises of several types of agents with well-defined behaviors which cooperate to fulfil the goal of the CPS subsystem. We evaluate the performance of the proposed approach using reliability metrics for a CPS aimed at monitoring ambient and environmental parameters.
Early acquisition of F0 alignment and scaling patterns in Catalan and Spanish

Six Catalan-speaking and six Spanish-speaking children between the ages of 24 and 48 months participated in a controlled naming task to elicit statement intonation patterns. A total of 127 utterances were prosodically analyzed using Cat_ToBI and Sp_ToBI ([1], [2]) and phonetic analyses of tonal alignment and scaling were performed. Our results show that children as young as two can finely control tonal alignment, corroborating some recent results for Catalan, Spanish, English, and European Portuguese ([3], [4], [5], [6]). Importantly, children show a more precise development of tonal alignment than tonal scaling. The f0 scaling results show that the youngest children do not produce the target L% boundary tone, confirming earlier observations on the high proportion of “level contours” in infant speech ([3], [4], [7]).
Effect of bottles, cups, and dummies on breast feeding in preterm infants: a randomised controlled trial

Abstract Objective To determine the effect of artificial teats (bottle and dummy) and cups on breast feeding in preterm infants. Design Randomised controlled trial. Setting Two large tertiary hospitals, 54 peripheral hospitals. Participants 319 preterm infants (born at 23-33 weeks' gestation) randomly assigned to one of four groups: cup/no dummy (n = 89), cup/dummy (n = 72), bottle/no dummy (n = 73), bottle/dummy (n = 85). Women with singleton or twin infants < 34 weeks' gestation who wanted to breastfeed were eligible to participate. Interventions Cup or bottle feeding occurred when the mother was unable to be present to breast feed. Infants randomised to the dummy groups received a dummy on entry into the trial. Main outcome measures Full breast feeding (compared with partial and none) and any breast feeding (compared with none) on discharge home. Secondary outcomes: prevalence of breast feeding at three and six months after discharge and length of hospital stay. Results 303 infants (and 278 mothers) were included in the intention to treat analysis. There were no significant differences for any of the study outcomes according to use of a dummy. Infants randomised to cup feeds were more likely to be fully breast fed on discharge home (odds ratio 1.73, 95% confidence interval 1.04 to 2.88, P = 0.03), but had a longer length of stay (hazard ratio 0.71, 0.55 to 0.92, P = 0.01). Conclusions Dummies do not affect breast feeding in preterm infants. Cup feeding significantly increases the likelihood that the baby will be fully breast fed at discharge home, but has no effect on any breast feeding and increases the length of hospital stay.