Miracle-dz/UniFAR-FTUs huggingface dataset:
Digits Lost or Gained? Evidence for Pedal Evolution in the Dwarf Salamander Complex (Eurycea, Plethodontidae)

Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages – the Eurycea quadridigitata complex (dwarf salamanders) – emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf−Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders) versus digit gain (re-evolution in the Edwards Plateau complex). Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.
The Quality of Reporting Methods and Results in Network Meta-Analyses: An Overview of Reviews and Suggestions for Improvement

Introduction Some have suggested the quality of reporting of network meta-analyses (a technique used to synthesize information to compare multiple interventions) is sub-optimal. We sought to review information addressing this claim. Objective To conduct an overview of existing evaluations of quality of reporting in network meta-analyses and indirect treatment comparisons, and to compile a list of topics which may require detailed reporting guidance to enhance future reporting quality. Methods An electronic search of Medline and the Cochrane Registry of methodologic studies (January 2004–August 2013) was performed by an information specialist. Studies describing findings from quality of reporting assessments were sought. Screening of abstracts and full texts was performed by two team members. Descriptors related to all aspects of reporting a network meta-analysis were summarized. Results We included eight reports exploring the quality of reporting of network meta-analyses. From past reviews, authors found several aspects of network meta-analyses were inadequately reported, including primary information about literature searching, study selection, and risk of bias evaluations; statement of the underlying assumptions for network meta-analysis, as well as efforts to verify their validity; details of statistical models used for analyses (including information for both Bayesian and Frequentist approaches); completeness of reporting of findings; and approaches for summarizing probability measures as additional important considerations. Conclusions While few studies were identified, several deficiencies in the current reporting of network meta-analyses were observed. These findings reinforce the need to develop reporting guidance for network meta-analyses. Findings from this review will be used to guide next steps in the development of reporting guidance for network meta-analysis in the format of an extension of the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analysis) Statement.
The regulation of photosynthetic electron transport during nutrient deprivation in Chlamydomonas reinhardtii.

The light-saturated rate of photosynthetic O2 evolution in Chlamydomonas reinhardtii declined by approximately 75% on a per-cell basis after 4 d of P starvation or 1 d of S starvation. Quantitation of the partial reactions of photosynthetic electron transport demonstrated that the light-saturated rate of photosystem (PS) I activity was unaffected by P or S limitation, whereas light-saturated PSII activity was reduced by more than 50%. This decline in PSII activity correlated with a decline in both the maximal quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers (PSII centers capable of performing a charge separation but unable to reduce the plastoquinone pool). In addition to a decline in the light-saturated rate of O2 evolution, there was reduced efficiency of excitation energy transfer to the reaction centers of PSII (because of dissipation of absorbed light energy as heat and because of a transition to state 2). These findings establish a common suite of alterations in photosynthetic electron transport that results in decreased linear electron flow when C. reinhardtii is limited for either P or S. It was interesting that the decline in the maximum quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers were regulated specifically during S-limited growth by the SacI gene product, which was previously shown to be critical for the acclimation of C. reinhardtii to S limitation (J.P. Davies, F.H. Yildiz, and A.R. Grossman [1996] EMBO J 15: 2150-2159).
‘HIV is an enemy of childbearers’: the construction of local epidemiology in rural Malawi

In the sub-Saharan African AIDS epidemic there is no shortage of formal messages about HIV distributed through health clinics, NGOs and the media. These messages, however, do not always address the issues that are of most importance for people living in the epidemic and learning how to navigate it safely. In rural Malawi, one message that has been absent concerns the implications of HIV for childbearing. Using data from in-depth interviews, this paper argues that rural Malawians socially constructed their own belief system and came to believe strongly that pregnancy and childbirth would negatively impact the disease progression of HIV-positive women. Through the recursive processes of selective observation, interpretation of formal public health messages and discussion within social networks, rural Malawians concluded that HIV and childbearing did not go together. In an uncertain world, social constructive processes such as these that are fluid and responsive to local circumstances are particularly important for making sense of the seemingly senseless and for developing tools to navigate unsettled times.
Persistent abdominal symptoms in US adults after short-term stay in Mexico.

BACKGROUND Postinfectious irritable bowel syndrome (PI-IBS) has been reported as a complication of bacterial diarrhea including travelers' diarrhea (TD). This study assessed the role of TD among US students in Mexico in triggering the onset of persistent abdominal symptoms (PAS) and IBS. METHODS We conducted a 6-month follow-up of a cohort of 817 US students in Mexico as short-term study to assess the frequency of PAS and IBS. Using Rome II criteria for IBS, groups of students with PAS were then categorized as PI-IBS if they met the symptom criteria for IBS or as suffering from functional abdominal disorder (FAD) if they did not meet the criteria. RESULTS FAD and IBS were commonly found in US students 6 months after leaving Mexico. Important variables in their development were younger adult age, longer stays in Mexico and occurrence of acute diarrhea while in Mexico. Diarrhea while in Mexico occurred more commonly for those later diagnosed with FAD, 101/196 (52%), relative risk (RR) = 1.5 [confidence interval (CI) 1.2-1.8; p = 0.001]; IBS, 20/32 (63%), RR = 2.5 (CI 1.2-5.0; p = 0.007); and PAS (FAD + IBS), 121/228 (53%), RR = 1.5 (CI 1.2-1.8; p < 0.001) compared with subjects who had experienced diarrhea while in Mexico but were not diagnosed with PAS at 6 months, 227/589 (39%). Diarrhea caused by heat-labile enterotoxin-producing enterotoxigenic Escherichia coli or Providencia ssp. demonstrated a greater risk of developing PAS. CONCLUSIONS PAS occurred commonly in a subset of younger adult travelers who stayed longer in Mexico and experienced acute diarrhea while there. Further studies with this cohort will focus on host genetic associations with the development of PAS.
On the Robust Dynamics Identification of Parallel Manipulators: Methodology and Experiments

The proposed chapter presents a self-contained approach for the dynamics identification of parallel manipulators. Major feature is the consequent consideration of structural properties of such machines in order to provide an experimentally adequate identification method. Thereby, we aim to achieve accurate model parameterization for control, simulation or analysis purposes. Despite the big progress made on identification of serial manipulators, it is interesting to state the missing of systematic identification methodologies for closed-loop and parallel kinematic manipulators (PKM’s). This is due to many factors that are discussed and treated systematically in this chapter. First, the issue of modelling the dynamics of PKM’s in a linear form with respect to the parameters to be identified is addressed. As it is already established in the field of classic serial robotics, such step is necessary to ensure model identifiability and to apply computationally efficient linear estimation (Swevers et al., 1997; Khalil & Dombre, 2002; Abdellatif & Heimann, 2007). The case of parallel manipulators is more complicated, since a multitude of coupled and closed kinematic chains has to be considered (Khalil & Guegan, 2004; Abdellatif et al., 2005a). Beside the rigid-body dynamics, friction plays a central role in modelling, since its accurate compensation yields important improvement of control accuracy. If friction in the passive joints is regarded, the dimension of the parameter vector grows and affects the estimation in a negative way. To cope with such problem, a method for the reduction of the friction parameter number is proposed, which is based on the identifiability analysis for a given manipulator structure and by considering the actual measurement noise. The calculation procedure of a dynamics model in minimal parametrized form is given in section 2. Another important issue of PKM’s is the appropriate design of the identification experiment, in order to obtain reliable estimation results. Two aspects are here crucial: The choice or the definition of the experiment framework at the one hand and its related experiment optimization at the other hand. Regarding the first aspect, the harmonic excitation approach proposed a couple of years ago for serial manipulators is chosen (Swevers et al., 1997). The method provides bounded motion that can be fitted in the usually highly restricted and small workspace of parallel robots. Thus, we propose an appropriate adaptation for PKM’s. The experiment optimization is carried out within a statistical frame in order to account for
Deep adversarial neural decoding

Here, we present a novel approach to solve the problem of reconstructing perceived stimuli from brain responses by combining probabilistic inference with deep learning. Our approach first inverts the linear transformation from latent features to brain responses with maximum a posteriori estimation and then inverts the nonlinear transformation from perceived stimuli to latent features with adversarial training of convolutional neural networks. We test our approach with a functional magnetic resonance imaging experiment and show that it can generate state-of-the-art reconstructions of perceived faces from brain activations.
Polymeric Multicomponent Materials: An Introduction

FUNDAMENTAL RELATIONSHIPS. Basic Concepts in Multicomponent Polymer Materials. Modeling Multicomponent Polymer Behavior. Fracture Behavior. POLYMER SURFACES AND INTERFACES. Basic Principles and Instruments. Polymer Chains at Surfaces and Interfaces. Strengthening the Interface. Surfaces of Advanced and Composite Systems. SELECTED ENGINEERING POLYMER MATERIAL. Rubber Toughening of Engineering Plastics. Block Copolymers and Thermoplastic Elastomers. Interpenetrating Polymer Networks. Overview and Future. Index.
List-decodable robust mean estimation and learning mixtures of spherical gaussians

We study the problem of list-decodable (robust) Gaussian mean estimation and the related problem of learning mixtures of separated spherical Gaussians. In the former problem, we are given a set T of points in n with the promise that an α-fraction of points in T, where 0< α < 1/2, are drawn from an unknown mean identity covariance Gaussian G, and no assumptions are made about the remaining points. The goal is to output a small list of candidate vectors with the guarantee that at least one of the candidates is close to the mean of G. In the latter problem, we are given samples from a k-mixture of spherical Gaussians on n and the goal is to estimate the unknown model parameters up to small accuracy. We develop a set of techniques that yield new efficient algorithms with significantly improved guarantees for these problems. Specifically, our main contributions are as follows: List-Decodable Mean Estimation. Fix any d ∈ + and 0< α <1/2. We design an algorithm with sample complexity Od ((nd/α)) and runtime Od ((n/α)d) that outputs a list of O(1/α) many candidate vectors such that with high probability one of the candidates is within ℓ2-distance Od(α−1/(2d)) from the mean of G. The only previous algorithm for this problem achieved error Õ(α−1/2) under second moment conditions. For d = O(1/), where >0 is a constant, our algorithm runs in polynomial time and achieves error O(α). For d = Θ(log(1/α)), our algorithm runs in time (n/α)O(log(1/α)) and achieves error O(log3/2(1/α)), almost matching the information-theoretically optimal bound of Θ(log1/2(1/α)) that we establish. We also give a Statistical Query (SQ) lower bound suggesting that the complexity of our algorithm is qualitatively close to best possible. Learning Mixtures of Spherical Gaussians. We give a learning algorithm for mixtures of spherical Gaussians, with unknown spherical covariances, that succeeds under significantly weaker separation assumptions compared to prior work. For the prototypical case of a uniform k-mixture of identity covariance Gaussians we obtain the following: For any >0, if the pairwise separation between the means is at least Ω(k+√log(1/δ)), our algorithm learns the unknown parameters within accuracy δ with sample complexity and running time (n, 1/δ, (k/)1/). Moreover, our algorithm is robust to a small dimension-independent fraction of corrupted data. The previously best known polynomial time algorithm required separation at least k1/4 (k/δ). Finally, our algorithm works under separation of Õ(log3/2(k)+√log(1/δ)) with sample complexity and running time (n, 1/δ, klogk). This bound is close to the information-theoretically minimum separation of Ω(√logk). Our main technical contribution is a new technique, using degree-d multivariate polynomials, to remove outliers from high-dimensional datasets where the majority of the points are corrupted.
SLC26A3 mutations in congenital chloride diarrhea

Congenital chloride diarrhea (CLD) is an autosomal recessive disorder of intestinal electrolyte absorption. It is characterized by persistent secretory diarrhea resulting in polyhydramnios and prematurity prenatally, and dehydration, hypoelectrolytemia, hyperbilirubinemia, abdominal distention, and failure to thrive immediately after birth. CLD is caused by mutations in the solute carrier family 26, member 3 gene (SLC26A3, alias CLD or DRA), which encodes a Na+‐independent Cl−/HCO3− (or OH−) exchanger. SLC26A3 is a member of the SLC26 sulfate permease/anion transporter family and it is expressed mainly in the apical brush border of intestinal epithelium. The only extraintestinal tissues showing SLC26A3 expression are eccrine sweat glands and seminal vesicles. A wide variety of different mutations in the SLC26A3 gene have been associated with CLD with no apparent evidence of phenotype–genotype correlation. The clinical course of CLD, however, is variable and may rather depend on environmental factors and compensatory mechanisms than mutations. In this report, we present a summary of all published and two novel SLC26A3 mutations and polymorphisms, and review them in the context of their functional consequences and clinical implications. Hum Mutat 20:425–438, 2002. © 2002 Wiley‐Liss, Inc.
A Three-Phase UPS That Complies With the Standard IEC 62040-3

This paper proposes a down-sampled discrete-time internal-model-based controller in the synchronous reference frame with a reduced number of poles. This controller is suitable for three-phase pulsewidth modulation inverters with output transformer for double-conversion uninterruptible power supply applications. It is demonstrated that the use of a down-sampled rate and fewer poles in the internal model results in a number of benefits, among which are the following: 1) improvement of the transient response; 2) increase of the stability margin of the closed-loop system; 3) a straightforward implementation in fixed-point digital signal processor (DSP) and microcontroller implementation as well as a reduction of the required memory space; and 4) a simple solution for the saturation of the output transformer. As a result, it is possible to obtain output voltages with reduced total harmonic distortion while ensuring good transient performance for both linear and nonlinear loads. To confirm the advantages claimed for the proposed synchronous reference dq frame internal-model-based controller and to demonstrate the steady-state and transient performance under the test conditions of the International electrotechnical commission standard 62040-3, the experimental results from a 10-kVA space-vector-modulated three-phase inverter, which is fully controlled by a DSP TMS320F241, are presented.
Effects of changing wrist positions on finger flexor hypertonia in stroke survivors

We sought to establish whether spastic hypertonia results from changes in intrinsic muscle properties or from altered stretch reflex properties. We hypothesized that finger flexor spastic hypertonia is primarily of neural origin, and that the dynamics of spastic muscle responses to stretch should therefore reflect the dynamics of muscle spindle receptor responses. In 12 stroke survivors, we recorded torque and electromyographic (EMG) responses of extrinsic finger flexors to constant‐velocity rotation of the metacarpophalangeal (MCP) joints of the affected hand, over a range of initial muscle lengths. Stretch velocity was set to 6°, 50°, 150°, or 300° per second. Muscle length changes were imposed by changing wrist angle between 0°, 25°, and 50° of flexion. We found that reflex torque and EMG responses exhibited both velocity and length dependence, and there were significant interactions between velocity and length, replicating known characteristics of muscle spindle receptors. Our results support the hypothesis that finger flexor hypertonia is primarily of neural origin, and that it accurately reflects spindle receptor firing properties. Muscle Nerve 2006
Extracellular Signal-Regulated Kinase Promotes Rho-Dependent Focal Adhesion Formation by Suppressing p190A RhoGAP

ABSTRACT Cell migration is critical for normal development and for pathological processes including cancer cell metastasis. Dynamic remodeling of focal adhesions and the actin cytoskeleton are crucial determinants of cell motility. The Rho family and the mitogen-activated protein kinase (MAPK) module consisting of MEK-extracellular signal-regulated kinase (ERK) are important regulators of these processes, but mechanisms for the integration of these signals during spreading and motility are incompletely understood. Here we show that ERK activity is required for fibronectin-stimulated Rho-GTP loading, Rho-kinase function, and the maturation of focal adhesions in spreading cells. We identify p190A RhoGAP as a major target for ERK signaling in adhesion assembly and identify roles for ERK phosphorylation of the C terminus in p190A localization and activity. These observations reveal a novel role for ERK signaling in adhesion assembly in addition to its established role in adhesion disassembly.
Mice Lacking the Alpha9 Subunit of the Nicotinic Acetylcholine Receptor Exhibit Deficits in Frequency Difference Limens and Sound Localization

Sound processing in the cochlea is modulated by cholinergic efferent axons arising from medial olivocochlear neurons in the brainstem. These axons contact outer hair cells in the mature cochlea and inner hair cells during development and activate nicotinic acetylcholine receptors composed of α9 and α10 subunits. The α9 subunit is necessary for mediating the effects of acetylcholine on hair cells as genetic deletion of the α9 subunit results in functional cholinergic de-efferentation of the cochlea. Cholinergic modulation of spontaneous cochlear activity before hearing onset is important for the maturation of central auditory circuits. In α9KO mice, the developmental refinement of inhibitory afferents to the lateral superior olive is disturbed, resulting in decreased tonotopic organization of this sound localization nucleus. In this study, we used behavioral tests to investigate whether the circuit anomalies in α9KO mice correlate with sound localization or sound frequency processing. Using a conditioned lick suppression task to measure sound localization, we found that three out of four α9KO mice showed impaired minimum audible angles. Using a prepulse inhibition of the acoustic startle response paradigm, we found that the ability of α9KO mice to detect sound frequency changes was impaired, whereas their ability to detect sound intensity changes was not. These results demonstrate that cholinergic, nicotinic α9 subunit mediated transmission in the developing cochlear plays an important role in the maturation of hearing.
Open Reduction and Internal Fixation of Tibial Pilon Fractures Using a Lateral Approach

Objectives: To assess the wound complications and reductions achieved in a cohort of patients with pilon fractures who were treated using a novel lateral approach. Design: Retrospective review. Setting: Two level 1 trauma centers affiliated with academic institutions. Patients/Methods: All 44 fractures (in 43 patients) treated by the senior authors with open reduction and internal fixation (ORIF) using the lateral approach as the primary approach were included. Intervention: Data regarding medical comorbidities, mechanism of injury, soft-tissue injury sustained during the injury, treatment, wound healing, and secondary surgeries were recorded. Fractures were classified using the AO/OTA system with most being type C3. Eighteen fractures were open injuries (10 type 3). Fracture reductions were scored using the criteria of Teeny and Wiss. Main Outcome Measurements: Quality of articular reduction and soft-tissue healing. Results: An anatomic or good fracture reduction was achieved in 41 fractures (93%), and a fair reduction was obtained in 3 fractures. Two patients were successfully treated for deep infection (4.5%), and 2 patients developed a wound dehiscence (4.5%). There were no amputations. Twelve patients underwent secondary surgeries (27%). Five of these were for symptomatic screw removal (related to the fibular hardware in all cases), and the sixth was for planned removal of a syndesmotic-type screw (13.6%). Four were for nonunion, representing 9% of all cases. The remaining secondary surgeries (2 cases) were performed for infection. Overall, 13.6% of patients underwent a secondary surgical procedure to address nonunion or infection. Conclusions: When applied in a staged fashion, the lateral surgical approach for pilon fractures provides excellent protection of the soft-tissue envelopes by creating thick flaps while allowing excellent visualization for reconstruction of the anterior and lateral distal tibia.