Miracle-dz/UniFAR-FTUs huggingface dataset:
When bigger is not better: selection against large size, high condition and fast growth in juvenile lemon sharks

Selection acting on large marine vertebrates may be qualitatively different from that acting on terrestrial or freshwater organisms, but logistical constraints have thus far precluded selection estimates for the former. We overcame these constraints by exhaustively sampling and repeatedly recapturing individuals in six cohorts of juvenile lemon sharks (450 age‐0 and 255 age‐1 fish) at an enclosed nursery site (Bimini, Bahamas). Data on individual size, condition factor, growth rate and inter‐annual survival were used to test the ‘bigger is better’, ‘fatter is better’ and ‘faster is better’ hypotheses of life‐history theory. For age‐0 sharks, selection on all measured traits was weak, and generally acted against large size and high condition. For age‐1 sharks, selection was much stronger, and consistently acted against large size and fast growth. These results suggest that selective pressures at Bimini may be constraining the evolution of large size and fast growth, an observation that fits well with the observed small size and low growth rate of juveniles at this site. Our results support those of some other recent studies in suggesting that bigger/fatter/faster is not always better, and may often be worse.
R-torsion and zeta functions for analytic Anosov flows on 3-manifolds

We improve previous results relating R-torsion, for an acyclic representation of the fundamental group, with a special value of the torsion zeta function of an analytic Anosov flow on a 3-manifold. By using the new techniques of Rugh and Fried we get rid of the unpleasent assumptions about the regularity of the invariant foliations.
Pronunciation modeling in speech synthesis

This dissertation investigates the area of pronunciation modeling in speech synthesis. By pronunciation modeling, we mean architectures and principles for generating high-quality human-like pronunciations. The term pronunciation modeling has previously been applied in the context of speech recognition (e.g. Byrne et al. 1997). In that context, it describes theories and procedures for handling the pronunciation variation that naturally occurs across speakers. In contrast, our work is in the domain of text-to-speech synthesis, which, as we will show, requires modeling the pronunciation variation of an individual whose speech the synthesizer is attempting to model. We will explain our methodology for learning and reproducing pronunciation variation on an individual basis, and show how most crucial features of such variation can be easily generated using the architecture we describe. Throughout the course of this exposition, we highlight contributions to linguistic theory that such a thorough analysis of individual variation provides. We describe the postlexical module of an English text-to-speech synthesizer. This module is responsible for transforming underlying lexical pronunciations from a lexical database into contextually appropriate surface postlexical pronunciations. This transformation is achieved by machine learning of a corpus of hand-labeled postlexical pronunciations that have been aligned with lexical pronunciations. The machine learning is conducted by a neural network, whose architecture and data encoding we describe. A thorough analysis of the performance of the postlexical module is offered, with attention to the relative success of the neural network at learning a wide range of postlexical phenomena. We examine the extent to which a symbolic approach to allophony is warranted, and provide an acoustic analysis that attempts to provide an answer to this question. Assessments of the success of currently existing theories of phonetics, phonology and their interface are offered, based on the experience of generating a complete postlexical phonology of English for use in synthetic speech. Comments University of Pennsylvania Institute for Research in Cognitive Science Technical Report No. IRCS-98-09. This thesis or dissertation is available at ScholarlyCommons: http://repository.upenn. edu/ircs_reports/55 PRONUNCIATION MODELING IN SPEECH SYNTHESIS
Where is the real transform boundary in California?

The zone of highest geodetically defined strain rate in California does not everywhere coincide with the surface trace of the San Andreas Fault (SAF). To determine whether this reflects the pattern of long‐term, permanent deformation, we analyzed the velocity field on swaths across the transform, located so as to avoid intersections among the major fault strands. Slip rates and flexural parameters for each fault were determined by finding the best fit to the velocity profile using a simple arctan model, representing the interseismic strain accumulation. Our slip rates compare well with current geologic estimates, which suggests that the present‐day velocity field is representative of long‐term motions. We find that the transform is a zone of high strain rate up to 80 km wide that is straighter than the SAF and has an overall trend closer to the relative plate motion vector than the SAF. Most sections of the SAF take up less than half of the total slip rate, and slip is transferred from one part of the system to another in a way that suggests that the SAF should not be considered as a unique locator of the plate boundary. Up to half of the total displacement takes place on faults outside the high strain rate zone, distributed over several hundred kilometers on either side. Our findings substantiate previous suggestions that the transform has the characteristics of a macroscopic ductile shear zone cutting the continental lithosphere, around which stress and strain rate decrease on a length scale controlled by the length of the transform.
Calcium pentosan polysulfate is a multifaceted exosite inhibitor of aggrecanases

Degradation of the cartilage proteoglycan aggrecan is a key early event in the development of osteoarthritis. Adamalysin with thrombospondin motifs (ADAMTS) −4 and ADAMTS‐5 are considered to be the main enzymes responsible for aggrecan breakdown, making them attractive drugs targets. Here we show that calcium pentosan polysulfate (CaPPS), a chemically sulfated xylanopyranose from beechwood, is a multifaceted exosite inhibitor of the aggrecanases and protects cartilage against aggrecan degradation. CaPPS interacts with the noncatalytic spacer domain of ADAMTS‐4 and the cysteine‐rich domain of ADAMTS‐5, blocking activity against their natural substrate aggrecan with inhibitory concentration 50 values of 10–40 nM but only weakly inhibiting hydrolysis of a nonglycosylated recombinant protein substrate. In addition, CaPPS increased cartilage levels of tissue inhibitor of metallo‐proteinases‐3 (TIMP‐3), an endogenous inhibitor of ADAMTS‐4 and −5. This was due to the ability of CaPPS to block endocytosis of TIMP‐3 mediated by low‐density lipoprotein receptor‐related protein. CaPPS also increased the affinity of TIMP‐3 for ADAMTS‐4 and −5 by more than 100‐fold, improving the efficacy of TIMP‐3 as an aggrecanase inhibitor. Studies with TIMP‐3‐null mouse cartilage indicated that CaPPS inhibition of aggrecan degradation is TIMP‐3 dependent. These unique properties make CaPPS a prototypic disease‐modifying agent for osteoarthritis. —Troeberg, L. , Fushimi, K. , Khokha, R. , Emonard, H. , Ghosh, P., Nagase, H. Calcium pentosan polysulfate is a multifaceted exosite inhibitor of aggrecanases. FASEB J. 22, 3515–3524 (2008)
What is the foundation of evidence of human factors decisions in language design? an empirical study on programming language workshops

In recent years, the programming language design community has engaged in rigorous debate on the role of empirical evidence in the design of general purpose programming languages. Some scholars contend that the language community has failed to embrace a form of evidence that is non-controversial in other disciplines (e.g., medicine, biology, psychology, sociology, physics, chemistry), while others argue that a science of language design is unrealistic. While the discussion will likely persist for some time, we begin here a systematic evaluation of the use of empirical evidence with human users, documenting, paper-by-paper, the evidence provided for human factors decisions, beginning with 359 papers from the workshops PPIG, Plateau, and ESP. This preliminary work provides the following contributions: an analysis of the 1) overall quantity and quality of empirical evidence used in the workshops, and of the 2) overall significant challenges to reliably coding academic papers. We hope that, once complete, this long-term research project will serve as a practical catalog designers can use when evaluating the impact of a language feature on human users.
An in vitro comparison of tracheostomy tube cuffs

Introduction The Shiley™ Flexible adult tracheostomy tube with TaperGuard™ cuff has been designed through its geometry, materials, diameter, and wall thickness to minimize micro-aspiration of fluids past the cuff and to provide an effective air seal in the trachea while also minimizing the risk of excessive contact pressure on the tracheal mucosa. The cuff also has a deflated profile that may allow for easier insertion through the stoma site. This unique design is known as the TaperGuard™ cuff. The purpose of the observational, in vitro study reported here was to compare the TaperGuard™ taper-shaped cuff to a conventional high-volume low-pressure cylindrical-shaped cuff (Shiley™ Disposable Inner Cannula Tracheostomy Tube [DCT]) with respect to applied tracheal wall pressure, air and fluid sealing efficacy, and insertion force. Methods Three sizes of tracheostomy tubes with the two cuff types were placed in appropriately sized tracheal models and lateral wall pressure was measured via pressure-sensing elements on the inner surface. Fluid sealing performance was assessed by inflating the cuffs within the tracheal models (25 cmH2O), instilling water above the cuff, and measuring fluid leakage past the cuff. To measure air leak, tubes were attached to a test lung and ventilator, and leak was calculated by subtracting the average exhaled tidal volume from the average delivered tidal volume. A tensile test machine was used to measure insertion force for each tube with the cuff deflated to simulate clinical insertion through a stoma site. Results The average pressure exerted on the lateral wall of the model trachea was lower for the taper-shaped cuff than for the cylindrical cuff under all test conditions (P<0.05). The taper-shaped cuff also demonstrated a more even, lower pressure distribution along the lateral wall of the model trachea. The average air and fluid seal performance with the taper-shaped cuff was significantly improved, when compared to the cylindrical-shaped cuff, for each tube size tested (P<0.05). The insertion force for the taper-shaped cuff was ~40% less than that for the cylindrical-shaped cuff. Conclusion In a model trachea, the Shiley™ Flexible Adult tracheostomy tube with TaperGuard™ cuff, when compared to the Shiley™ Disposable Inner Cannula Tracheostomy tube with cylindrical cuff, exerted a lower average lateral wall pressure and a more evenly distributed pressure. In addition, it provided more effective fluid and air seals and required less force to insert.
Immediate implant placement in molar regions: risk factors for early failure.

OBJECTIVES To identify risk factors for early failure of immediately placed implants in molar regions associated with three bone regenerative techniques. METHODS Ninety-two patients (44 women and 48 men; mean age 50 years, 35 smokers and 57 non-smokers) in need of a single implant crown to replace a molar were included. After placing the implant, patients were randomized to one of three treatment groups for bone reconstruction of remaining periimplant defects: Autologous bone (AB) chips, Ossix membrane (OM) or a combination of AB chips and OM. The implant was submerged, and after 4 months of healing a re-entry surgery was made to connect a healing abutment. Implants with a dehiscence on ≥2 sites (mesial/distal/oral/buccal) together with ≥50% visible threads, were judged as failures. A series of simple logistic regression analyses were performed to identify risk factors for failure among the following independent variables: sex, jaw, smoking status, plaque, bleeding on probing, fistula, extraction reason, mean initial periimplant defect size, treatment group, implant length, buccal bone dehiscence (BBD), soft-tissue dehiscence and infection. The identified risk factors entered a multiple logistic regression analysis. RESULTS Fifteen implants failed before abutment operation (13 explantations/two non-osseointegrated). Treatment group had no impact on failure. Risk factors for failure were: Smoking >10 cigarettes/day (odds ratio [OR]=9.29, confidence interval [CI]=1.21-71.16), BBD (OR=11.43, CI=1.34-97.74) and infection (OR=36.7, CI=2.75-489.31). CONCLUSIONS Implants placed immediately after extraction of a molar were associated with a high risk for failure at abutment operation. There was no difference in failure rate between three bone reconstructive techniques.
Bipedal reflex coordination to tactile stimulation of the sural nerve during human running.

1. Cutaneous reflex responses were elicited during human running (8 km/h) on a treadmill by electrical stimulation of the sural nerve at the ankle. Stimulus trains (5 pulses of 1 ms at 200 Hz) at three nonnociceptive intensities, which were 1.5, 2.0, and 2.5 times perception threshold (PT), were delivered at 16 phases of the step cycle. For 11 subjects the surface electromyographic (EMG) activity of both the ipsilateral and contralateral long head of the biceps femoris (iBF and cBF, respectively), the semitendinosus (iST and cST), the rectus femoris (iRF and cRF), and the tibialis anterior (iTA and cTA) were recorded. 2. During human running nonnociceptive sural nerve stimulation appears to be sufficient to elicit large, widespread and statistically significant reflex responses, with a latency of approximately 80 ms and a duration of approximately 30 ms. These reflex responses seem to be an elementary property of human locomotion. This is indicated by the occurrence of the responses in all subjects, the consistency of most of the reflex patterns across the subjects and, apart from a small amount of habituation, the reproducibility of the responses during the course of the experiment. 3. The responses are modulated continuously throughout the step cycle such that their magnitude does not in general covary with the background locomotor activities. This is observed most clearly in iST, iTA, and cTA for which statistically significant reflex reversals are demonstrated, and in cRF and cTA for which the responses are gated during most of the step cycle. 4. The response magnitude generally increases as a function of increasing intensity, whereas the phase-dependent reflex modulation is intensity independent. 5. A functional dissociation within the ipsilateral hamstring muscles is demonstrated: the iBF and iST show an antagonistic reflex pattern (facilitatory and suppressive, respectively) during the periods of synergistic background locomotor activity in the step cycle. Contralaterally, however, the cBF and cST are reflexively activated as close synergists during these periods. 6. The reflex responses and their phase-dependent modulation are different for the homologous muscles in the two legs. Yet, some similarities are observed. These are present rather with respect to the phase of the corresponding leg than with respect to the phase of the stimulated leg. Both observations suggest that the phase-dependent reflex modulation is controlled separately in the ipsilateral and contralateral legs. 7. The response simultaneity in all investigated muscles supports the notion of a coordinated cutaneous interlimb reflex during human running. (ABSTRACT TRUNCATED AT 400 WORDS)
Gene Set Signature of Reversal Reaction Type I in Leprosy Patients

Leprosy reversal reactions type 1 (T1R) are acute immune episodes that affect a subset of leprosy patients and remain a major cause of nerve damage. Little is known about the relative importance of innate versus environmental factors in the pathogenesis of T1R. In a retrospective design, we evaluated innate differences in response to Mycobacterium leprae between healthy individuals and former leprosy patients affected or free of T1R by analyzing the transcriptome response of whole blood to M. leprae sonicate. Validation of results was conducted in a subsequent prospective study. We observed the differential expression of 581 genes upon exposure of whole blood to M. leprae sonicate in the retrospective study. We defined a 44 T1R gene set signature of differentially regulated genes. The majority of the T1R set genes were represented by three functional groups: i) pro-inflammatory regulators; ii) arachidonic acid metabolism mediators; and iii) regulators of anti-inflammation. The validity of the T1R gene set signature was replicated in the prospective arm of the study. The T1R genetic signature encompasses genes encoding pro- and anti-inflammatory mediators of innate immunity. This suggests an innate defect in the regulation of the inflammatory response to M. leprae antigens. The identified T1R gene set represents a critical first step towards a genetic profile of leprosy patients who are at increased risk of T1R and concomitant nerve damage.
Ephemeral and intermittent runoff generation processes in a low relief, highly weathered catchment

Most field‐based approaches that address runoff generation questions have been conducted in steep landscapes with shallow soils. Runoff generation processes in low relief landscapes with deep soils remain less understood. We addressed this by characterizing dominant runoff generating flow paths by monitoring the timing and magnitude of precipitation, runoff, shallow soil moisture, and shallow and deep groundwater dynamics in a 3.3 ha ephemeral‐to‐intermittent drainage network in the Piedmont region of North Carolina, USA. This Piedmont region is gently sloped with highly weathered soils characterized by shallow impeding layers due to decreases in saturated hydraulic conductivity with depth. Our results indicated two dominant catchment storage states driven by seasonal evapotranspiration. Within these states, distinct flow paths were activated, resulting in divergent hydrograph recessions. Groundwater dynamics during precipitation events with different input characteristics and contrasting storage states showed distinct shallow and deep groundwater flow path behavior could produce similar runoff magnitudes. During an event with low antecedent storage, activation of a shallow, perched, transient water table dominated runoff production. During an event with high antecedent storage, the deeper water table activated shallow flow paths by rising into the shallow transmissive soil horizons. Despite these differing processes, the relationship between active surface drainage length (ASDL) and runoff was consistent. Hysteretic behavior between ASDL and runoff suggested that while seasonal ASDLs can be predicted based on runoff, the mechanisms and source areas producing flow can be highly variable and not easily estimated from runoff alone. These processes and flow paths have significant implications for stream chemistry across seasons and storage states.
An Automatic Hybrid Method for Retinal Blood Vessel Extraction

An Automatic Hybrid Method for Retinal Blood Vessel Extraction The extraction of blood vessels from retinal images is an important and challenging task in medical analysis and diagnosis. This paper presents a novel hybrid automatic approach for the extraction of retinal image vessels. The method consists in the application of mathematical morphology and a fuzzy clustering algorithm followed by a purification procedure. In mathematical morphology, the retinal image is smoothed and strengthened so that the blood vessels are enhanced and the background information is suppressed. The fuzzy clustering algorithm is then employed to the previous enhanced image for segmentation. After the fuzzy segmentation, a purification procedure is used to reduce the weak edges and noise, and the final results of the blood vessels are consequently achieved. The performance of the proposed method is compared with some existing segmentation methods and hand-labeled segmentations. The approach has been tested on a series of retinal images, and experimental results show that our technique is promising and effective.
Familiarity differentially affects right hemisphere contributions to processing metaphors and literals

The role of the two hemispheres in processing metaphoric language is controversial. While some studies have reported a special role of the right hemisphere (RH) in processing metaphors, others indicate no difference in laterality relative to literal language. Some studies have found a role of the RH for novel/unfamiliar metaphors, but not conventional/familiar metaphors. It is not clear, however, whether the role of the RH is specific to metaphor novelty, or whether it reflects processing, reinterpretation or reanalysis of novel/unfamiliar language in general. Here we used functional magnetic resonance imaging (fMRI) to examine the effects of familiarity in both metaphoric and non-metaphoric sentences. A left lateralized network containing the middle and inferior frontal gyri, posterior temporal regions in the left hemisphere (LH), and inferior frontal regions in the RH, was engaged across both metaphoric and non-metaphoric sentences; engagement of this network decreased as familiarity decreased. No region was engaged selectively for greater metaphoric unfamiliarity. An analysis of laterality, however, showed that the contribution of the RH relative to that of LH does increase in a metaphor-specific manner as familiarity decreases. These results show that RH regions, taken by themselves, including commonly reported regions such as the right inferior frontal gyrus (IFG), are responsive to increased cognitive demands of processing unfamiliar stimuli, rather than being metaphor-selective. The division of labor between the two hemispheres, however, does shift towards the right for metaphoric processing. The shift results not because the RH contributes more to metaphoric processing. Rather, relative to its contribution for processing literals, the LH contributes less.
Selective Anti-Proliferation of HER2-Positive Breast Cancer Cells by Anthocyanins Identified by High-Throughput Screening

Overexpressed Human epidermal growth factor receptor 2 (HER2) drives the biology of 20% breast cancer and is a prediction of a poor prognosis for patients. HER2-targeted therapies significantly improve outcomes for HER2-positive patients. Traditional Chinese herbs/medicines have been used to treat breast cancer patients including HER2-positive patients in Asia for decades. Although the traditional medicines demonstrate efficacy in clinics for HER2-positive patients, the mechanism is largely unknown. In this article, we screened a 10,000 natural product library in 6 different cell lines representing breast cancer, and assessed the ability of each drug to cause cytotoxicity through a high-throughput screening approach. We have identified eight natural compounds that selectively inhibit the proliferation of HER2-positive cells. Two of the hit compounds, peonidin-3-glucoside and cyaniding-3-glucoside, are both extracts from black rice. They inhibit the phospho-HER2 and phospho-AKT and were confirmed to induce HER2-psotive breast cancer cells apoptosis both in vitro and in vivo. Peonidin-3-glucoside and cyaniding-3-glucoside treatments significantly reduced the tumor size and volume in vivo compared to the control group. There is no significant difference of antitumorgenic effects between peonidin-3-glucoside and cyaniding-3-glucoside treatments.