Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncovering Higher‐Taxon Diversification Dynamics from Clade Age and Species‐Richness Data

Abstract The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time‐dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age), and taxonomic delimitation can affect estimates of the age‐richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations. To assess its informative breadth, we characterize ARC behavior with simulated and empirical phylogenies, considering phylogenetic structure and both crown and stem ages. First, we develop a two‐state birth‐death model to simulate phylogenies including the origin of higher taxa and a hierarchical taxonomy to determine ARC expectations under ecologically and time‐dependent diversification processes. Then, we estimate ARCs across various taxonomic ranks of extant amphibians, squamate reptiles, mammals, birds, and flowering plants. We find that our model reproduces the general ARC trends of a wide range of biological systems despite the particularities of taxonomic practice within each, suggesting that the model is adequate to establish a framework of ARC null expectations for different diversification processes when taxa are defined with a hierarchical taxonomy. ARCs estimated with crown ages were positive in all the scenarios we studied, including ecologically dependent processes. Negative ARCs were only found at less inclusive taxonomic ranks, when considering stem age, and when rates varied among clades. This was the case both in ecologically and time‐dependent processes. Together, our results warn against direct interpretations of single ARC estimates and advocate for a more integrative use of ARCs across age types and taxonomic ranks in diversification studies.
UvA-DARE (Digital Academic Repository) ‘Knowable’ as ‘known after an announcement’

Public announcement logic is an extension of multiagent epistemic logic with dynamic operators to model the informational consequences of announcements to the entire group of agents. We propose an extension of public announcement logic with a dynamic modal operator that expresses what is true after any announcement: 3 ϕ expresses that there is a truthful announcement ψ after which ϕ is true. This logic gives a perspective on Fitch’s knowability issues: For which formulas ϕ , does it hold that ϕ → 3 K ϕ ? We give various semantic results and show completeness for a Hilbert-style axiomatization of this logic. There is a natural generalization to a logic for arbitrary events.
3-Year Follow-up of Clinical and Behavioral Improvements Following a Multifaceted Diabetes Care Intervention

Purpose The purpose of this study was to determine if improvements observed in clinical, behavioral, and psychosocial outcomes measured at 12 months following a multifaceted diabetes care intervention were sustained at 3-year follow-up. Methods This study was a multilevel, nonblinded, cluster design, randomized controlled trial that took place in an under-served suburb of Pittsburgh, Pennsylvania, between 1999 and 2005. Eleven primary care practices, and their patients, were randomly assigned to 3 groups: chronic care model (CCM) intervention (n = 30), provider education only (PROV) (n = 38), and usual care (UC) (n = 51). Subjects were followed for 3 years. Results Improvements observed at 12-month follow-up in glycemic (—0.5%) and blood pressure control (—4.8 mm Hg), and the proportion of participants who self-monitor their blood glucose (86.7%-100%), were sustained at 3-year follow-up in the CCM group. Additional improvements occurred in non-HDLc levels in all study groups and quality of well-being scores in the CCM intervention group. All associations remained after controlling for medication treatment intensification. Conclusions We have demonstrated that improvements in outcomes can be sustained over time following a multifaceted diabetes care intervention. Future research in this area is necessary to understand if improvements in outcomes can be sustained following diabetes self-management education (DSME) and what type of patient fares the best from multifaceted diabetes care interventions.
Shoukhrat Mitalipov and Masahito Tachibana's Mitochondrial Gene Replacement Therapy Technique

In 2009, their team researchers developed the technology of mitochondrial gene replacement therapy to prevent the transmission of a mitochondrial disease from mother to offspring in primates. Mitochondria contain some of the body's genetic material, called mitochondrial DNA. Occasionally, the mitochondrial DNA possesses mutations. Mitalipov and Tachibana, researchers Beaverton, Oregon, developed a technique to remove the nucleus [3] of the mother and place it in a donor oocyte [4] , or immature egg [5] cell, with healthy mitochondria. The resulting offspring contain the genetic material of three separate individuals and do not have the disease. Mitalipov and Tachibana's technology of mitochondrial gene replacement built on decades of research by different scientists and enables researchers to prevent the transmission of human mitochondrial diseases from mother to offspring. Mitochondrial gene replacement therapy enables researchers to remove mutated mitochondria. Mitochondria are the organelles found in cells that provide energy for cells to function. Mitochondria contain a small portion of the cell's genetic material, called the mitochondrial DNA, or mtDNA. Mitochondrial DNA is comprised of thirty-seven genes [6] responsible for energy production and cell function. Mitochondria are passed down from mother to offspring, meaning that offspring receives maternal mitochondrial DNA. Occasionally, the mother's mitochondrial DNA contains mutations, which often leads to mitochondrial disease. Because there are no known treatments for mitochondrial diseases, researchers experimented with ways to prevent the transmission of mutated mitochondrial DNA to offspring. transplanted tadpole oocytes with embryonic nuclei resulted in healthy tadpoles that later developed into frogs. King's
Modeling and evaluation of single machine flexibility using fuzzy entropy and genetic algorithm based approach

Flexibility has long been recognized as a manufacturing capability that has the potential to impact mainly the competitive position of an organization. The entropy approach, which was extended from information theory, fell in handling problems with incomplete and uncertain data, because it depicts only the stochastic aspects included with measured observations. In order to get a global view, this work proposes a new approach based on fuzzy entropy concept. The development of the fuzzy model results in a set of nonlinear constrained problems to be solved using a metaheuristics method. The applicability of our approach is illustrated through a flexible manufacturing cell. By adopting such framework, both dimensions of uncertainty in system modeling, expressed by stochastic variability and imprecision, can be taken into consideration.
Error Bounds of Adaptive Dynamic Programming Algorithms for Solving Undiscounted Optimal Control Problems

In this paper, we establish error bounds of adaptive dynamic programming algorithms for solving undiscounted infinite-horizon optimal control problems of discrete-time deterministic nonlinear systems. We consider approximation errors in the update equations of both value function and control policy. We utilize a new assumption instead of the contraction assumption in discounted optimal control problems. We establish the error bounds for approximate value iteration based on a new error condition. Furthermore, we also establish the error bounds for approximate policy iteration and approximate optimistic policy iteration algorithms. It is shown that the iterative approximate value function can converge to a finite neighborhood of the optimal value function under some conditions. To implement the developed algorithms, critic and action neural networks are used to approximate the value function and control policy, respectively. Finally, a simulation example is given to demonstrate the effectiveness of the developed algorithms.
Transcanal Endoscopic Ear Surgery for Excision of a Facial Nerve Venous Malformation With Interposition Nerve Grafting: A Case Report.

OBJECTIVE To illustrate a novel approach for the surgical management of a venous malformation of the facial nerve, including interposition nerve grafting, via an exclusively transcanal endoscopic ear surgery (TEES) approach. PATIENT Thirty nine-year-old woman with a preoperative House-Brackmann (HB) grade IV facial paresis secondary to a facial nerve tumor. INTERVENTION(S) Surgical excision and interposition nerve graft via a transcanal endoscopic approach. MAIN OUTCOME MEASURE(S) Completeness of resection, approach morbidities, and facial nerve outcome. RESULTS The TEES approach provided wide exposure of the facial nerve from the geniculate ganglion through the mastoid segment. This visualization facilitated gross total tumor resection, incus interposition ossicular reconstruction, and placement of an interposition nerve graft. The nerve graft was positioned in the fallopian canal and was secured at both ends with surgicel. The patient had no postoperative complications. At 11-month follow-up her facial function had returned to HB grade IV. CONCLUSIONS This is the first report of resecting a venous malformation of the facial nerve with concomitant interposition nerve graft reconstruction via an exclusively endoscopic approach. This report adds to the growing body of evidence that TEES can manage diverse middle ear and lateral skull base pathology. Additional studies are needed to fully elucidate the risk-benefit profile of this technique.
Consensus of Multi-agent Systems with Time Delays and Measurement Noises

In this paper, the leader-following consensus problem of high order multi-agent systems with time-varying communication delays and noises is considered. The interconnection topology among the agents is assumed to be switching and undirected. The dynamics of each agent and the leader is a linear system. To track the active leader, a neighbor-based control of each following agent is designed in using local information. The control design technique is based on algebraic graph theory, Riccati inequality and Lyapunov inequality. By using Lyapunov-Razumikhim and stochastic analysis methods, we prove that the closed loop tracking control system is stochastically stable in mean square and the estimation errors converge to zero in mean square as well. Finally, a numerical example is given to illustrate the obtained result. DOI: http://dx.doi. org/10.11591/telkomnika.v10i6. 1429 Full Text: PDF
Association of vitamin D status with semen quality and reproductive hormones in Iranian subfertile men

Although vitamin D deficiency is one of the most common health problems throughout the world, including Iran, conflicting information exists on the potential association between serum vitamin D levels and semen quality. This study intended to evaluate the association between serum vitamin D [25(OH) D3] with semen quality and hormones in Iranian subfertile men. We also compared mean vitamin D and hormone levels in normospermic men with oligoasthenoteratozoospermia (OAT) men. This cross‐sectional study was conducted on 278 men who were referred to Royan Infertility Clinic (Tehran, Iran) from March to September 2014. The participants were categorized into two groups; of 186 normospermic and 92 OAT patients according to World Health Organization 2010 criteria. Each participant provided informed consent prior to launching research. Participants completed two general questionnaires of nutritional status. Blood and semen samples were obtained for assessment, and all data were adjusted for age, body mass index (BMI), and season. Vitamin D levels were classified according to Institute of Medicine guidelines. Vitamin D deficiency, insufficiency, and normal levels were observed in 8.6%, 43.6%, 47.8% of participants, respectively. No association was found between daily dietary intake of vitamin D and calcium with sperm parameters. Serum vitamin D was inversely correlated with PTH (p < 0.045). In normospermic men, serum vitamin D levels categorized were not correlated with semen parameters and reproductive hormones (FSH, LH, testosterone(T), and FT), whereas sperm motility showed a positive correlation with vitamin D categorized in OAT men (rs = 0.131, p = 0.028). In conclusion, there was a high incidence of deficiency and insufficiency 25(OH) D Levels (<20ng/ml) observed in Iranian men (52.2%). Moreover, our findings showed a correlation between vitamin D levels and sperm motility in OAT men, which requires further studies.
Analysis and design of full-bridge Class-DE inverter at fixed duty cycle

This paper presents the following for a full-bridge Class-DE resonant inverter operating at a fixed duty ratio: (a) steady-state analysis using first-harmonic approximation and (b) derivation of closed-form expressions for the currents, voltages, and powers. The conversion from a series-parallel resonant network to a series resonant network is presented. Imposing the zero-voltage and zero-derivative switching conditions, the expression for a shunt capacitance across the MOSFETs in the inverter bridge is derived. The closed-form expressions to calculate the values of the resonant components are presented. A practical design of a Class-DE resonant inverter supplied by a dc input voltage of 230 V, delivering an output power of 920 W, and operating at a switching frequency of 100 kHz is considered and its design methodology is included. Theoretical results are validated by Saber simulations.
Stereo from uncalibrated cameras

The problem of computing placement of points in 3-D space, given two uncalibrated perspective views, is considered. The main theorem shows that the placement of the points is determined only up to an arbitrary projective transformation of 3-space. Given additional ground control points, however, the location of the points and the camera parameters may be determined. The method is linear and noniterative, whereas previously known methods for solving the camera calibration and placement problem to take proper account of both ground-control points and image correspondences are unsatisfactory in requiring either iterative methods or model restrictions. As a result of the main theorem, it is possible to determine projective invariants of 3-D geometric configurations from two perspective views. <<ETX>>
An image representation based convolutional network for DNA classification

The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary DNA sequence, though the interaction is not yet fully understood. In this paper we develop a convolutional neural network that takes an image-representation of primary DNA sequence as its input, and predicts key determinants of chromatin structure. The method is developed such that it is capable of detecting interactions between distal elements in the DNA sequence, which are known to be highly relevant. Our experiments show that the method outperforms several existing methods both in terms of prediction accuracy and training time.
Dynamic motion capture and edition using a stack of tasks

This paper presents a complete methodology to quickly reshape a dynamic motion demonstrated by a human and to adapt the dynamics of the human to the dynamics of the robot. The method uses an inverse dynamics control scheme with a quadratic programming optimization solver. The motion data recorded using a motion capture system is introduced into the control scheme as a reference posture task to be followed by the joints trajectory respecting the dynamic limitations as well as the contact constraints. The motion is further modified using arbitrary tasks to let the robot imitate the original motion more closely or to make voluntary changes for aesthetic reasons. The results show the method applied to the humanoid robot HRP-2 imitating a human “pop dance”.
An exploration of Singaporean parental experiences in managing school-aged children's postoperative pain: a descriptive qualitative approach.

AIMS AND OBJECTIVES To enhance understanding of the experience of parents in managing their children's postoperative pain in Singapore. BACKGROUND Parents play a significant role in their hospitalised child's postoperative pain care. Their active involvement may contribute to accurate pain assessment and effective pain management for their child. However, there is a lack of in-depth research exploring the experience of parents involved in their children's postoperative pain management. DESIGN This study adopted a descriptive qualitative approach, which is situated in the interpretive paradigm. METHOD Semi-structured interviews were conducted to collect data from 14 parents whose children were hospitalised in one of the three paediatric surgical wards in a hospital in Singapore in December 2009. Thematic analysis was used to analyse the data. RESULTS Three themes were identified: 'Actions used by parents to alleviate their child's postoperative pain', 'Factors influencing parents' management of their child's postoperative pain' and 'Parents' needs in the process of caring for their child's postoperative pain'. Parents used a range of non-pharmacological pain relief interventions for their child. Parental roles and expectations, bond between parent and child, support from nurses, family and own religious beliefs, as well as children's age and maturity level were factors which promoted parental participation, whereas parents' negative feelings, knowledge deficit and nurses' busy schedule were hindering factors. Parents expressed needs for more involvement in their child's care, adequate rest and information support from nurses. CONCLUSIONS This study highlights the importance of involving parents in their child's postoperative pain management. It provides evidence for health care professionals to pay attention to factors that may influence parental participation and, therefore, guide their practice. RELEVANCE TO CLINICAL PRACTICE Nurses need to provide parents with support and education to facilitate their roles and improve their child's postoperative pain management.
Effect of heat stress on the gene expression of ion transporters/channels in the uterus of laying hens during eggshell formation

Abstract Heat stress is a problem in laying hens as it decreases egg quality by decreasing eggshell mineralization. Heat stress alters gene expression, hence our aim was to investigate effects of heat stress on gene expression of ion transport elements involving in uterine mineralization (TRPV6, CALB1, ITPR3, SCNN1G, SLC4A4, KCNJ15, SLC4A9, and CLCN2) by real time quantitative PCR. Forty 23-week-old White Leghorn laying hens were housed in two rooms. The control group (n = 20) was maintained at 21–23 °C, and the heat stress group (n = 20) was exposed to 36–38 °C for 8 weeks. All parameters of egg quality including egg weight, surface area, volume, and eggshell weight, thickness, ash weight, and calcium content were decreased in the heat stress group compared to the control group (by 26.9%, 32.7%, 44.1%, 38.4%, 31.7%, 39.4%, and 11.1%, respectively). Total plasma calcium was decreased by 13.4%. Levels of ITPR3, SLC4A4, and SLC4A9 transcripts in the uterine lining were decreased in the heat stress group compared to the control group (by 61.4%, 66.1%, and 66.1%, respectively). CALB1 transcript level was increased (by 34.2 fold) in the heat stress group of hens compared to controls. TRPV6, SCNN1G, KCNJ15, and CLCN2 transcript levels did not significantly differ between control and heat stress groups of laying hens. It is concluded that the down-expression of ITPR3, SLC4A4, and SLC4A9 genes may impair transportation of Cl−, HCO3−, and Na+ in eggshell mineralization during heat stress. Increased CALB1 gene expression may increase resistance of uterine cells to detrimental effects of heat stress.
Some Common Mistakes In IR Evaluation, And How They Can Be Avoided

This paper points out some mistakes that can be frequently found in IR publications: MRR and ERR violate basic requirements for a metric, MAP is based on unrealistic assumptions, the numbers shown overstate the precision of the result, relative improvements of arithmetic means are inappropriate, the simple holdout method yields unreliable results, hypotheses are often formulated after the experiment, significance tests frequently ignore the multiple comparisons problem, effect sizes are ignored, reproducibility of the experiments might be nearly impossible, and sometimes authors claim proof by experimentation.
ON THE FERMI-GBM EVENT 0.4 s AFTER GW150914

In view of the recent report by Connaughton et al., we analyze continuous time-tagged event (TTE) data of Fermi-gamma-ray burst monitor (GBM) around the time of the gravitational-wave event GW 150914. We find that after proper accounting for low-count statistics, the GBM transient event at 0.4 s after GW 150914 is likely not due to an astrophysical source, but consistent with a background fluctuation, removing the tension between the INTEGRAL/ACS non-detection and GBM. Additionally, reanalysis of other short GRBs shows that without proper statistical modeling the fluence of faint events is over-predicted, as verified for some joint GBM–ACS detections of short GRBs. We detail the statistical procedure to correct these biases. As a result, faint short GRBs, verified by ACS detections, with significances in the broadband light curve even smaller than that of the GBM–GW150914 event are recovered as proper non-zero source, while the GBM–GW150914 event is consistent with zero fluence.
Shear Wave Wavefront Mapping Using Ultrasound Color Flow Imaging

A wavefront reconstruction method for a continuous shear wave is proposed. The method uses ultrasound color flow imaging (CFI) to detect the shear wave’s wavefront. When the shear wave vibration frequency satisfies the required frequency condition and the displacement amplitude satisfies the displacement amplitude condition, zero and maximum flow velocities appear at the shear wave vibration phases of zero and π rad, respectively. These specific flow velocities produce the shear wave’s wavefront map in CFI. An important feature of this method is that the shear wave propagation is observed in real time without addition of extra functions to the ultrasound imaging system. The experiments are performed using a 6.5 MHz CFI system. The shear wave is excited by a multilayer piezoelectric actuator. In a phantom experiment, the shear wave velocities estimated using the proposed method and those estimated using a system based on displacement measurement show good agreement.