bluuebunny/crossref_metadata_2025_split huggingface dataset:
The word learning profile of adults with developmental language disorder
Authors: McGregor Karla K , Arbisi-Kelm Timothy , Eden Nichole , Oleson Jacob 
Published: January 2020

Background and aims Previous investigations of word learning problems among people with developmental language disorder suggest that encoding, not retention, is the primary deficit. We aimed to replicate this finding; test the prediction that word form, not the linking of form to referent, is particularly problematic; and determine whether women with developmental language disorder are better word learners than men with developmental language disorder. Methods Twenty adults with developmental language disorder and 19 age-, sex-, and education-matched peers with typical language development attempted to learn 15 words by retrieval practice. Their retention was measured one day-, one week-, and one month after training. Results The participants with developmental language disorder required more exposures to the word-referent pairs than the participants with typical language development to reach mastery. While training to mastery, they made more errors in word form production, alone or in combination with errors in linking forms to the correct referents, but the number of no attempts and pure link errors did not differ by group. Women demonstrated stronger retention of the words than men at all intervals. The developmental language disorder and typical language development groups did not differ at the one-day- and one-month retention intervals but the developmental language disorder group was weaker at the one-week interval. Review via retrieval practice at the one-day and one-week interval enhanced retention at the one-month interval; the review at one week was more beneficial than the review at one day. Women benefitted more from the review opportunities than men but the developmental language disorder and typical language development groups did not differ. Conclusions Adults with developmental language disorder present with weaknesses in the encoding of new words but retention is a relative strength. Encoding word forms is especially challenging but encoding word-to-referent links is not. We interpret this profile, and the evidence of a female advantage, as consistent with the Procedural Circuit Deficit Hypothesis. Implications: When treating a client with developmental language disorder whose goal is to increase vocabulary knowledge, the interventionist should anticipate the need for multiple exposures to new words within activities that highlight the forms of the words and support their memory and production. Periodic review should serve to support long-term retention.
Managing thromboembolic risk in patients with hereditary and acquired thrombophilias
Authors: Moran Jason , Bauer Kenneth A. 
Published: January 2020

Abstract
While we are now able to diagnose inherited thrombophilias in a substantial number of patients with venous thromboembolism (VTE), the initial hope that their presence would inform recurrence risk and thus decisions on anticoagulation duration has largely been disappointing. Indeed, the presence or absence of transient provoking risk factors has proven to be the most important determinant of VTE recurrence risk. Thus, particular attention to transient acquired risk factors for VTE remains paramount, as they have generally been shown to carry more prognostic weight than inherited thrombophilias. The presence of other acquired risk factors may require additional management considerations, whether pertaining to anticoagulant choice, as in antiphospholipid antibody syndrome, or to addressing a new predisposing medical condition, as in malignancy. Antithrombin deficiency or the presence of ≥1 thrombophilic defect may be exceptions that can have a role in prognostication; however, as illustrated in this review through several case vignettes, interpretation and clinical application of the results of inherited thrombophilia testing is nuanced. We have chosen to focus on cases in which patients have been identified as having thrombophilic defects rather than the indications for undertaking testing in the first place or the extent of investigation. Management decisions in such cases ultimately hinge on individualized consideration of the benefits and risks of anticoagulation along with patient preference rather than on an algorithmic pathway based on thrombophilia status.
Treatment of unusual thrombotic manifestations
Authors: Abbattista Maria , Capecchi Marco , Martinelli Ida 
Published: January 2020

Abstract
Venous thrombosis rarely occurs at unusual sites such as cerebral, splanchnic, upper-extremity, renal, ovarian, or retinal veins. Clinical features, symptoms, and risk factors of rare thrombotic manifestations are heterogeneous and in large part differ from those typical of the commonest manifestations of venous thrombosis at the lower extremities. The therapeutic approach also varies widely according to the affected site, whether cerebral, abdominal, or extraabdominal. To date, anticoagulant therapy for thrombosis at unusual sites is generally accepted, but the optimal therapeutic approach remains challenging. This review is focused on the treatment of unusual thrombotic manifestations as reported in the most recent guidelines and according to the updated scientific literature.
Acute treatment of venous thromboembolism
Authors: Becattini Cecilia , Agnelli Giancarlo 
Published: January 2020

Abstract
All patients with venous thromboembolism (VTE) should receive anticoagulant treatment in the absence of absolute contraindications. Initial anticoagulant treatment is crucial for reducing mortality, preventing early recurrences, and improving long-term outcome. Treatment and patient disposition should be tailored to the severity of clinical presentation, to comorbidities, and to the potential to receive appropriate care in the outpatient setting. Direct oral anticoagulants (DOACs) used in fixed doses without laboratory monitoring are the agents of choice for the treatment of acute VTE in the majority of patients. In comparison with conventional anticoagulation (parenteral anticoagulants followed by vitamin K antagonists), these agents showed improved safety (relative risk [RR] of major bleeding, 0.61; 95% confidence interval [CI], 0.45-0.83) with a similar risk of recurrence (RR, 0.90; 95% CI, 0.77-1.06). Vitamin K antagonists or low molecular weight heparins are still alternatives to DOACs for the treatment of VTE in specific patient categories such as those with severe renal failure or antiphospholipid syndrome, or cancer, respectively. In addition to therapeutic anticoagulation, probably less than 10% of patients require reperfusion by thrombolysis or interventional treatments; those patients are hemodynamically unstable with acute pulmonary embolism, and a minority of them have proximal limb-threatening deep vein thrombosis (DVT). The choice of treatment should be driven by the combination of evidence from clinical trials and by local expertise. The majority of patients with acute DVT and a proportion of selected hemodynamically stable patients with acute pulmonary embolism can be safely managed as outpatients.
Long-term treatment of venous thromboembolism
Authors: Kearon Clive , Kahn Susan R. 
Published: January 2020

Abstract
The most important decision in the long-term treatment of venous thromboembolism (VTE) is how long to anticoagulate. VTE provoked by a reversible risk factor, or a first unprovoked isolated distal deep vein thrombosis (DVT), generally should be treated for 3 months. VTE provoked by a persistent or progressive risk factor (eg, cancer), or a second unprovoked proximal DVT or PE, is generally treated indefinitely. First unprovoked proximal DVT or PE may be treated for 3 to 6 months or indefinitely. Male sex, presentation as PE (particularly if concomitant proximal DVT), a positive d-dimer test after stopping anticoagulation, an antiphospholipid antibody, low risk of bleeding, and patient preference favor indefinite anticoagulation. The type of indefinite anticoagulation is of secondary importance. Low-dose oral Xa inhibitors are convenient and are thought to have a lower risk of bleeding; they are less suitable if there is a higher risk for recurrence. For cancer-associated VTE, we now prefer full-dose oral Xa inhibitors over low-molecular-weight heparin, with gastrointestinal lesions being a relative contraindication. Graduated compression stockings are not routinely indicated after DVT, but are encouraged if there is persistent leg swelling or if a trial of stockings improves symptoms. Medications have a limited role in the treatment of postthrombotic syndrome. After PE, patients should have clinical surveillance for chronic thromboembolic pulmonary hypertension (CTEPH), with ventilation-perfusion scanning and echocardiography being the initial diagnostic tests if CTEPH is a concern. Patients with CTEPH and other symptomatic patients with extensive residual perfusion defects should be evaluated for endarterectomy, balloon pulmonary angioplasty, or vasodilator therapies.
Highly Efficient Synthesis of Carbon-Based Molybdenum Phosphide Nanoparticles for Electrocatalytic Hydrogen Evolution
Authors: Li Yang , Cai Lun , Huang Qilin , Liu Jun , Tang Ranran , Zhou Wenhan 
Published: January 2020

AbstractMolybdenum phosphide in transition metal phosphides members are considered as an attractive electrocatalyst for hydrogen evolution reaction (HER). However, its unsatisfactory stability and conductivity in an alkaline environment has dragged on its development. Here, we successfully introduced N, C co-doped MoP (MoP-NC) nanoparticles by a simple and efficient two-step synthesis method using urea as a carbon source into the molybdenum phosphide system. The cheapness of urea and the excellent carbon to nitrogen ratio remove the obstacles ahead of the development of MoP-NC composites. The obtained composites have excellent HER electrocatalytic activity and stability in 1-M potassium hydroxide (KOH) solution, which requires only an overpotential of 131 mV to achieve a current density of 10 mA cm−2 and exhibits negligible performance degradation after 1000 CV cycles.
Students’ “teleological misconceptions” in evolution education: why the underlying design stance, not teleology per se, is the problem
Authors: Kampourakis Kostas 
Published: January 2020

AbstractTeleology, explaining the existence of a feature on the basis of what it does, is usually considered as an obstacle or misconception in evolution education. Researchers often use the adjective “teleological” to refer to students’ misconceptions about purpose and design in nature. However, this can be misleading. In this essay, I explain that teleology is an inherent feature of explanations based on natural selection and that, therefore, teleological explanations are not inherently wrong. The problem we might rather address in evolution education is not teleology per se but the underlying “design stance”. With this I do not refer to creationism/intelligent design, and to the inference to a creator from the observation of the apparent design in nature (often described as the argument from design). Rather, the design stance refers to the intuitive perception of design in nature in the first place, which seems to be prevalent and independent from religiosity in young ages. What matters in evolution education is not whether an explanation is teleological but rather the underlying consequence etiology: whether a trait whose presence is explained in teleological terms exists because of its selection for its positive consequences for its bearers, or because it was intentionally designed, or simply needed, for this purpose. In the former case, the respective teleological explanation is scientifically legitimate, whereas in the latter case it is not. What then should be investigated in evolution education is not whether students provide teleological explanations, but which consequence etiologies these explanations rely upon. Addressing the design stance underlying students’ teleological explanations could be a main aim of evolution education.
Multi-year maintenance planning framework using multi-attribute utility theory and genetic algorithms
Authors: Allah Bukhsh Zaharah , Stipanovic Irina , Doree Andre G. 
Published: January 2020

AbstractThis paper introduces a comprehensive framework for the development of optimal multi-year maintenance plans for a large number of bridges. A maintenance plan is said to be optimal when, within the given budget, a maximum number of bridges can be maintained in the best possible year, achieving maximum performance with minimum socio-economic impact. The framework incorporates heuristic rules, multi-attribute utility theory, discrete Markov chain process, and genetic algorithms to find an optimal balance between limited budgets and performance requirements. The applicability of the proposed framework is illustrated on an extensive case study of highway bridges. The framework enables asset owners to execute various planning scenarios under different budget and performance requirements, where each resulting plan is optimal. The focus of this study has mainly been on highway bridges, however the framework is general and can be applied to any other infrastructure asset type.
DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment
Authors: Fukuda Hiroyuki , Tomii Kentaro 
Published: January 2020

Abstract
Background
Recently developed methods of protein contact prediction, a crucially important step for protein structure prediction, depend heavily on deep neural networks (DNNs) and multiple sequence alignments (MSAs) of target proteins. Protein sequences are accumulating to an increasing degree such that abundant sequences to construct an MSA of a target protein are readily obtainable. Nevertheless, many cases present different ends of the number of sequences that can be included in an MSA used for contact prediction. The abundant sequences might degrade prediction results, but opportunities remain for a limited number of sequences to construct an MSA. To resolve these persistent issues, we strove to develop a novel framework using DNNs in an end-to-end manner for contact prediction.

Results
We developed neural network models to improve precision of both deep and shallow MSAs. Results show that higher prediction accuracy was achieved by assigning weights to sequences in a deep MSA. Moreover, for shallow MSAs, adding a few sequential features was useful to increase the prediction accuracy of long-range contacts in our model. Based on these models, we expanded our model to a multi-task model to achieve higher accuracy by incorporating predictions of secondary structures and solvent-accessible surface areas. Moreover, we demonstrated that ensemble averaging of our models can raise accuracy. Using past CASP target protein domains, we tested our models and demonstrated that our final model is superior to or equivalent to existing meta-predictors.

Conclusions
The end-to-end learning framework we built can use information derived from either deep or shallow MSAs for contact prediction. Recently, an increasing number of protein sequences have become accessible, including metagenomic sequences, which might degrade contact prediction results. Under such circumstances, our model can provide a means to reduce noise automatically. According to results of tertiary structure prediction based on contacts and secondary structures predicted by our model, more accurate three-dimensional models of a target protein are obtainable than those from existing ECA methods, starting from its MSA. DeepECA is available from https://github.com/tomiilab/DeepECA.
Integrative analysis of time course metabolic data and biomarker discovery
Authors: Jendoubi Takoua , Ebbels Timothy M. D. 
Published: January 2020

AbstractBackgroundMetabolomics time-course experiments provide the opportunity to understand the changes to an organism by observing the evolution of metabolic profiles in response to internal or external stimuli. Along with other omic longitudinal profiling technologies, these techniques have great potential to uncover complex relations between variations across diverse omic variables and provide unique insights into the underlying biology of the system. However, many statistical methods currently used to analyse short time-series omic data are i) prone to overfitting, ii) do not fully take into account the experimental design or iii) do not make full use of the multivariate information intrinsic to the data or iv) are unable to uncover multiple associations between different omic data. The model we propose is an attempt to i) overcome overfitting by using a weakly informative Bayesian model, ii) capture experimental design conditions through a mixed-effects model, iii) model interdependencies between variables by augmenting the mixed-effects model with a conditional auto-regressive (CAR) component and iv) identify potential associations between heterogeneous omic variables by using a horseshoe prior.ResultsWe assess the performance of our model on synthetic and real datasets and show that it can outperform comparable models for metabolomic longitudinal data analysis. In addition, our proposed method provides the analyst with new insights on the data as it is able to identify metabolic biomarkers related to treatment, infer perturbed pathways as a result of treatment and find significant associations with additional omic variables. We also show through simulation that our model is fairly robust against inaccuracies in metabolite assignments. On real data, we demonstrate that the number of profiled metabolites slightly affects the predictive ability of the model.ConclusionsOur single model approach to longitudinal analysis of metabolomics data provides an approach simultaneously for integrative analysis and biomarker discovery. In addition, it lends better interpretation by allowing analysis at the pathway level. An accompanying package for the model has been developed using the probabilistic programming language . The package offers user-friendly functions for simulating data, fitting the model, assessing model fit and postprocessing the results. The main aim of the package is to offer freely accessible resources for integrative longitudinal analysis for metabolomics scientists and various visualization functions easy-to-use for applied researchers to interpret results.
Fossils from South China redefine the ancestral euarthropod body plan
Authors: Aria Cédric , Zhao Fangchen , Zeng Han , Guo Jin , Zhu Maoyan 
Published: January 2020

AbstractBackgroundEarly Cambrian Lagerstätten from China have greatly enriched our perspective on the early evolution of animals, particularly arthropods. However, recent studies have shown that many of these early fossil arthropods were more derived than previously thought, casting uncertainty on the ancestral euarthropod body plan. In addition, evidence from fossilized neural tissues conflicts with external morphology, in particular regarding the homology of the frontalmost appendage.ResultsHere we redescribe the multisegmented megacheiransFortiforcepsandJianfengiaand describeSklerolibyon maomimagen. et sp. nov., which we place in Jianfengiidae, fam. nov. (in Megacheira, emended). We find that jianfengiids show high morphological diversity among megacheirans, both in trunk ornamentation and head anatomy, which encompasses from 2 to 4 post-frontal appendage pairs. These taxa are also characterized by elongate podomeres likely forming seven-segmented endopods, which were misinterpreted in their original descriptions. Plesiomorphic traits also clarify their connection with more ancestral taxa. The structure and position of the “great appendages” relative to likely sensory antero-medial protrusions, as well as the presence of optic peduncles and sclerites, point to an overall homology with the anterior head of radiodontans. This is confirmed by our Bayesian phylogeny, which places jianfengiids as the basalmost euarthropods, paraphyletic with other megacheirans, and in contiguity with isoxyids and radiodontans.ConclusionsSklerolibyonand other jianfengiids expand the disparity of megacheirans and suggest that the common euarthropod ancestor possessed a remarkable phenotypic variability associated with the externalized cephalon, as well as endopods that were already heptopodomerous, which differs from previous hypotheses and observations. These animals also demonstrate that the frontalmost pair of arthrodized appendage is homologous between radiodontans and megacheirans, refuting the claim that the radiodontan frontal appendages evolved into the euarthropod labrum, and questioning its protocerebral identity. This evidence based on external anatomy now constitutes a solid benchmark upon which we should address issues of homology, with the help of carefully examined palaeoneurological data.
Adaptive divergence in shell morphology in an ongoing gastropod radiation from Lake Malawi
Authors: Van Bocxlaer Bert , Ortiz-Sepulveda Claudia M. , Gurdebeke Pieter R. , Vekemans Xavier 
Published: January 2020

Abstract
Background
Ecological speciation is a prominent mechanism of diversification but in many evolutionary radiations, particularly in invertebrates, it remains unclear whether supposedly critical ecological traits drove or facilitated diversification. As a result, we lack accurate knowledge on the drivers of diversification for most evolutionary radiations along the tree of life. Freshwater mollusks present an enigmatic example: Putatively adaptive radiations are being described in various families, typically from long-lived lakes, whereas other taxa represent celebrated model systems in the study of ecophenotypic plasticity. Here we examine determinants of shell-shape variation in three nominal species of an ongoing ampullariid radiation in the Malawi Basin (Lanistes nyassanus, L. solidus and Lanistes sp. (ovum-like)) with a common garden experiment and semi-landmark morphometrics.

Results
We found significant differences in survival and fecundity among these species in contrasting habitats. Morphological differences observed in the wild persisted in our experiments for L. nyassanus versus L. solidus and L. sp. (ovum-like), but differences between L. solidus and L. sp. (ovum-like) disappeared and re-emerged in the F1 and F2 generations, respectively. These results indicate that plasticity occurred, but that it is not solely responsible for the observed differences. Our experiments provide the first unambiguous evidence for genetic divergence in shell morphology in an ongoing freshwater gastropod radiation in association with marked fitness differences among species under controlled habitat conditions.

Conclusions
Our results indicate that differences in shell morphology among Lanistes species occupying different habitats have an adaptive value. These results also facilitate an accurate reinterpretation of morphological variation in fossil Lanistes radiations, and thus macroevolutionary dynamics. Finally, our work testifies that the shells of freshwater gastropods may retain signatures of adaptation at low taxonomic levels, beyond representing an evolutionary novelty responsible for much of the diversity and disparity in mollusks altogether.