Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient coupling of Sec23-Sec24 to Sec13-Sec31 drives COPII-dependent collagen secretion and is essential for normal craniofacial development

The COPII coat assembles on endoplasmic reticulum membranes to coordinate the collection of secretory cargo with the formation of transport vesicles. During COPII assembly, Sar1 deforms the membrane and recruits the Sec23-Sec24 complex (Sec23/24), which is the primary cargo-binding adaptor for the system, and Sec13-Sec31 (Sec13/31), which provides a structural outer layer for vesicle formation. Here we show that Sec13 depletion results in concomitant loss of Sec31 and juxtanuclear clustering of pre-budding complexes containing Sec23/24 and cargo. Electron microscopy reveals the presence of curved coated profiles on distended endoplasmic reticulum, indicating that Sec13/31 is not required for the generation or maintenance of the curvature. Surprisingly, export of tsO45-G-YFP, a marker of secretory cargo, is unaffected by Sec13/31 depletion; by contrast, secretion of collagen from primary fibroblasts is strongly inhibited. Suppression of Sec13 expression in zebrafish causes defects in proteoglycan deposition and skeletal abnormalities that are grossly similar to the craniofacial abnormalities of crusher mutant zebrafish and patients with cranio-lenticulo-sutural dysplasia. We conclude that efficient coupling of the inner (Sec23/24) and outer (Sec13/31) layers of the COPII coat is required to drive the export of collagen from the endoplasmic reticulum, and that highly efficient COPII assembly is essential for normal craniofacial development during embryogenesis.
Running head : SELECTION OF AUXILIARY VARIABLES 1 Selection of auxiliary variables in missing data problems : Not all auxiliary variables are created equal

The treatment of missing data in the social sciences has changed tremendously during the last decade. Modern missing data techniques such as multiple imputation and full-information maximum likelihood are used much more frequently. These methods assume that data are missing at random. One very common approach to increase the likelihood that missing at random is achieved, consists of including many covariates as so-called auxiliary variables. These variables are either included based on data considerations or in an inclusive fashion, i.e., taking all available auxiliary variables. However, neither approach accounts for the fact that under a wide range of circumstances there is a class of variables that, when used as auxiliary variables, will always increase bias in the estimation of parameters from data with missing values. In this paper we show that this bias exists, quantify it in a simulation study, and discuss possible ways how one can avoid selecting bias-inducing covariates as auxiliary variables.
Måleegenskaper ved den norske versjonen av Eyberg Child Behavior Inventory (ECBI)

Description. Eyberg Child Behavior Inventory (ECBI) was developed in the US during the 1970’ (Eyberg & Ross, 1978) as a parent rating scale to assess behavior problems in children aged 3-16 years. ECBI was translated from English to Norwegian by Willy-Tore Morch, the Arctic University of Norway. Psychological Assessment Resources (PAR) in USA distributes licenses needed to use the inventory. The ECBI can be utilized as a tool for screening, for clinical use, as well as for research purposes. It provides a list of 36 problem behaviors commonly reported by parents. The inventory assesses behavior on two dimensions, the frequency of the behavior and whether parents consider it as a problem. The frequency ratings range from 1 (never) to 7 (always), and are summed up to make an overall problem behavior Intensity Score ranging from 36 to 252. The problem identification assessment requires the parent to respond “yes” or “no” to the question: “Is this behavior a problem for you? ” The total Problem Score ranges from 0 to 36, and is calculated by summing the number of problems indicated by the parents. Scores from the Intensity Scale are used to evaluate the child’s behavior, whereas scores from the Problem Scale are utilized to evaluate which challenges the child pose on primary caregivers. It takes about 10- 15 minutes to complete the ECBI. There is no need for certification in order to administer the ECBI, except test-specific competence. Literature search. A total of 12 studies were included in this review; 11 Norwegian studies and one Swedish. These studies were conducted with children aged 4-9 years in both clinical and universal populations. PsykTestBarn 2011, 1:11 http://www.r-bup.no/CMS/ptb.nsf/pages/ecbi 3 Psychometrics. Psychometrical data consisted of mean values, standard deviations in representative norms groups, subgroups and clinical samples, as well as internal consistency and explorative factor analyses. Conclusion The ECBI has very good reliability as well as Norwegian norms from a representative sample. Some evidence lends support to the construct validity of the test.
Medical Diagnosis Using Ensemble Classifiers - A Novel Machine-Learning Approach

In designing high-performance computer-aided diagnosis systems, improving the accuracies of the machine-learning algorithms is vital, and ensemble data-mining methods (EDMM), learning algorithms having a combination of multiple base models, are the most suggested methods. In the present study, the experiments are conducted on five medical datasets and the results justify that there is a drastic enhancement in the performance of the base classifiers, and this certainly would facilitate effective medical diagnosis, which in turn would contribute to the health index of the patients. Further, it is concluded that only selected classifiers are to be used for each data set, and for some specified cases, ensemble classifiers need not be proposed. A proper selection of the classifier is recommended in order to achieve optimal accuracy with regard to a specific medical data set.
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny

The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists–how can one assign relative dates to the vertices of the tree? In this paper we investigate this problem, as suming a uniform distribution on the order of the inner vertices of the tree (which includes, but is more general than, the popular Yule distribution on trees). We derive fast algorithms for computing the probability that (i) any given vertex in the tree was the j–th speciation event (for each j), and (ii) any one given vertex is earlier in the tree than a second given vertex. We show how the first algorithm can be used to calculate the expected length of any given interior edge in any given tree that has been generated under either a constant- rate speciation model, or the coalescent model.
Photolithographic Micropatterning of Conducting Polymers on Flexible Silk Matrices

UNLABELLED High-resolution micropatterning of a PEDOT PSS conducting-polymer-silksericin composite is presented using a water-based, benchtop photolithographic process. Conducting microstructures formed on a flexible silk fibroin sheet allow a fully organic, flexible bioelectronic device. Large-area microfabricated devices such as biosensors that are biocompatible and degradable over a controlled period of time can be formed.
Early in vivo Effects of the Human Mutant Amyloid-β Protein Precursor (hAβPPSwInd) on the Mouse Olfactory Bulb.

The amyloid-β protein precursor (AβPP) has long been linked to Alzheimer's disease (AD). Using J20 mice, which express human AβPP with Swedish and Indiana mutations, we studied early pathological changes in the olfactory bulb. The presence of AβPP/amyloid-β (Aβ) was examined in mice aged 3 months (before the onset of hippocampal Aβ deposition) and over 5 months (when hippocampal Aβ deposits are present). The number of neurons, non-neurons, and proliferating cells was assessed using the isotropic fractionator method. Our results demonstrate that although AβPP is overexpressed in some of the mitral cells, widespread Aβ deposition and microglia aggregates are not prevalent in the olfactory bulb. The olfactory bulbs of the younger J20 group harbored significantly fewer neurons than those of the age-matched wild-type mice (5.57±0.13 million versus 6.59±0.36 million neurons; p = 0.011). In contrast, the number of proliferating cells was higher in the young J20 than in the wild-type group (i.e., 6617±425 versus 4455±623 cells; p = 0.011). A significant increase in neurogenic activity was also observed in the younger J20 olfactory bulb. In conclusion, our results indicate that (1) neurons participating in the mouse olfactory function overexpress AβPP; (2) the cellular composition of the young J20 olfactory bulb is different from that of wild-type littermates; (3) these differences may reflect altered neurogenic activity and/or delayed development of the J20 olfactory system; and (4) AβPP/Aβ-associated pathological changes that take place in the J20 hippocampus and olfactory bulb are not identical.
Invited Reflection

Intersectionality has traveled far from its historical moorings in the reflections of Black feminists such as Sojourner Truth (1851) and the Combahee River Collective (1977). It has journeyed through the academy in the work of Black feminist scholars such as Kimberlé Crenshaw (1989, 1991) and Patricia Hill Collins (1991) and in recent years has landed within diverse disciplines, including psychology. Alas, touching down in a discipline as conventional as mainstream psychology brings a host of challenges for designing and conducting quantitative research pursuant to a framework not developed to be operationalized, measured, or empirically tested (Syed, 2010). Until now, researchers have relied primarily on qualitative methods to investigate intersectionality, raising a host of questions about the epistemological and methodological fit—not to mention pragmatics—of conducting quantitative intersectionality research (Bowleg, 2008; Cole, 2009). In a series of exciting developments, however, scholars from disciplines as diverse as epidemiology (Bauer, 2014), political science (Hancock, 2007), and psychology (Warner, 2008) have advanced critiques and insightful guidelines for conducting intersectionality research quantitatively. In a welcomed addition to this list, enter feminist psychologists Else-Quest and Hyde (2016) with a substantive examination of some key methodological and technical considerations for the discipline of psychology. Building on the strengths of Else-Quest and Hyde’s article, our commentary seeks to expand their work in three areas: (1) a more explicit emphasis on power and social–structural context, (2) advocacy for mixed methods, and (3) more attention to the structural realities of sampling and recruitment. We also discuss our fundamental disagreement with Else-Quest and Hyde’s description of multiple main effects as representing an intersectionality approach.
An EMG controlled prosthetic forearm in three degrees of freedom using ultrasonic motors

This paper discusses an EMG controlled prosthetic forearm with three degrees of freedom actuated by small size ultrasonic motors. Its weight is less than 700 g and the size is the same as the adult's forearm. It produces no motion noise. In addtion, it is possible to control six kinds of motions i.e. pronation and supnation of the forearm, flection and extension of the wrist, and grasping and hand-opening.
Convergence of Least Squares Temporal Difference Methods Under General Conditions

We consider approximate policy evaluation for finite state and action Markov decision processes (MDP) in the off-policy learning context and with the simulation-based least squares temporal difference algorithm, LSTD(λ). We establish for the discounted cost criterion that the off-policy LSTD(λ) converges almost surely under mild, minimal conditions. We also analyze other convergence and boundedness properties of the iterates involved in the algorithm, and based on them, we suggest a modification in its practical implementation. Our analysis uses theories of both finite space Markov chains and Markov chains on topological spaces.
Towards minimizing the annotation cost of certified text classification

The common practice of testing a sequence of text classifiers learned on a growing training set, and stopping when a target value of estimated effectiveness is first met, introduces a sequential testing bias. In settings where the effectiveness of a text classifier must be certified (perhaps to a court of law), this bias may be unacceptable. The choice of when to stop training is made even more complex when, as is common, the annotation of training and test data must be paid for from a common budget: each new labeled training example is a lost test example. Drawing on ideas from statistical power analysis, we present a framework for joint minimization of training and test annotation that maintains the statistical validity of effectiveness estimates, and yields a natural definition of an optimal allocation of annotations to training and test data. We identify the development of allocation policies that can approximate this optimum as a central question for research. We then develop simulation-based power analysis methods for van Rijsbergen's F-measure, and incorporate them in four baseline allocation policies which we study empirically. In support of our studies, we develop a new analytic approximation of confidence intervals for the F-measure that is of independent interest.
Physiological Correlates of Stress in Individuals about to Undergo Eye Laser Surgery

We examined to what extent we can distinguish between 'real-life' stressed and relaxed participants on the basis of heart rate (HR), heart rate variability (HRV) and skin conductance level (SCL) as measured during rest. Physiological and subjective measures were compared between individuals that were to undergo eye laser surgery and a control group. We found significantly higher HR and lower HRV in surgery clients, but no effect on SCL. Moreover, physiological indicators (HR) were found to correlate with subjective ones. Despite the inter-subject variations we were able to discriminate (using an SVM classifier) between surgery clients and controls with an accuracy of 70%. An alternative method of measuring HR using a Vital Signs camera showed good correspondence (error of 0.50 bpm in mean HR) with HR determined from ECG, opening up a range of practical applications that require contact less measurement methods.
Conditions for the stability of wireless ARQ protocols and reliable communications

We consider ARQ protocols which vary the error probabilities per retransmission, having no channel state information at the transmitter. Such protocols can be described by irreducible and aperiodic discrete time Markov chains with countably infinite states of a specific form. Ergodicity of such chains guarantees finite expected delay until correct reception as well as positive throughput. Initiating from general stability criteria we formulate and prove necessary and sufficient conditions for recurrence, ergodicity and non-ergodicity for the chains of interest. The conditions are applied to the case of retransmissions via a Rayleigh fading channel to obtain recurrence and ergodicity conditions based on power allocation per retransmission.
Simulations studies of multisensor track association and fusion methods

Recent work has developed maximum likelihood (ML) methods for track-to-track data association and fusion in a multisensor, i.e., more than two sensor, environment. In order to conserve bandwidth, only the state estimates and corresponding covariance matrices are shared amongst the nodes. The fusion engine uses this track information to determine which tracks associate to the same target and then computes a fused track to improve the accuracy of the state estimates. The simplest class of ML methods assumes that the track errors from different sensors are uncorrelated. The more computationally demanding ML methods incorporate the cross-correlations that are due to the common process noise in the kinematic model of the target. In order to account for track correlations in practice, the cross-covariance matrices must be approximated from the single sensor covariance matrices. This paper introduces new methods to approximate the cross-covariance matrices, and these approximations lead to a third class of association and estimation methods. The paper then uses simulations to assess the performance of the different association and estimation techniques. The simulations include results when the sensor tracks are produced by either a Kalman filter or an interacting multiple model (IMM) filter
Literal and figurative meanings of Spanish spatial prepositions in Chinese students’ acquisition of Spanish as a third language

This thesis investigates the acquisition of the spatial and figurative meanings of five Spanish spatial particles, namely sobre, encima, debajo, bajo and en, by a group of Chinese university students of Spanish as a foreign language at intermediate and upper-intermediate language levels. More specifically, this study aims to answer two questions. The first question considers the order of acquisition of prepositional meanings, that is, whether this is similar to a native language, with literal and more primary meanings acquired first and figurative ones later or, conversely, whether the pattern of acquisition is different to that found in a first language (Kemmerer, 2005; Lam, 2010). The second question of this research is to determine whether there are observable differences between the degree of acquisition and use of these prepositions in English compared to Spanish, and if so, what the characteristics of these differences are. To try to answer these questions, the performance of this group of participants in four behavioural tests is compared. The tests were a lexical identification task, a picture fillin-theblank task, a sentence generation task and a truth value judgment task. These tests were conducted both in Spanish, which the participants had begun to study at vi undergraduate level and English, which they had first been exposed to in school in a prepuberty period. The results of this study indicate, first, that the acquisition of the literal and figurative meanings of the spatial particles in this study does not follow a pattern similar to that found in a native language. That is, meaning acquisition in a foreign language occurs in a parallel or simultaneous pattern. Furthermore, in a non-immersion context such as that of this study, the age at which students begin the study of a foreign language is not a decisive factor in determining the degree of mastery that students can obtain. The quantity and quality of the input students are exposed to; together with an appropriate methodology appear to be the most important factors in predicting the level of proficiency that can be reached.
Integrated semantic search in the product development phase

Finding relevant and needed information within company's specific repositories or internet resources has become a time consuming part of the development process. In order to optimally exploit the large amounts of engineering information one of the key challenges is, that an engineer has to be aware of proper keywords and all kind of relevant repositories in order to start a successful search. Especially with respect to unstructured repositories such as fileservers an explicit search process becomes complicated, time consuming and sometimes impossible, due to the lack of appropriate metadata. By combining existing technologies from the areas of natural language processing, search engines and desktop integration frameworks a concept for an integrated semantic search tool is proposed, where a user has not to be aware of the repositories and their specifics. As an intermediate result, we present a prototypical implementation, where the knowledge retrieval process is initiated in the background on basis of an automatic identification of a selected text paragraph and its semantic similarity to existing documents in an unstructured repository. This way the system delivers valuable context specific documents just by a simple click.
Patient coping and expectations about recovery predict the development of chronic post-surgical pain after traumatic tibial fracture repair.

BACKGROUND The association of patient expectations about recovery with the development of chronic post-surgical pain (CPSP) is uncertain. METHODS Three hundred and fifty-nine patients enrolled in the SPRINT trial completed the Somatic Preoccupation and Coping (SPOC) questionnaire six weeks after a traumatic tibial fracture repair. The SPOC questionnaire measures patients' somatic complaints, coping, and optimism for recovery. Using adjusted models, we explored the association of SPOC scores with ≥ mild CPSP and ≥ moderate pain interference with activity at one yr after surgery. RESULTS Of 267 tibial fracture patients with data available for analysis, 147 (55.1%) reported CPSP at one yr. The incidence of CPSP was 37.6% among those with low (≤40) SPOC scores, 54.1% among those with intermediate (41-80) scores, and 81.7% among those with high (>80) scores. Addition of SPOC scores to an adjusted regression model to predict CPSP improved the c-statistic from 0.61 (95% CI 0.55-0.68) to 0.70 (95% CI 0.64-0.76, P=0.005 for the difference) and found the greatest risk was associated with high SPOC scores (OR 6.56, 95% CI 2.90-14.81). Similarly, an adjusted regression model to predict pain interference with function at one yr (c-statistic 0.77, 95% CI 0.71-0.83) found the greatest risk for those with high SPOC scores (OR 10.10, 95% CI 4.26-23.96). CONCLUSIONS Patient's coping and expectations of recovery, as measured by the SPOC questionnaire, is an independent predictor of CPSP and pain interference one yr after traumatic tibial fracture. Future studies should explore whether these beliefs can be modified, and if doing so improves prognosis. CLINICAL TRIAL REGISTRATION NCT 00038129.
Activation of Akt (Protein Kinase B) in Mammary Epithelium Provides a Critical Cell Survival Signal Required for Tumor Progression

ABSTRACT Activation of Akt by the phosphatidylinositol 3′-OH kinase (PI3K) results in the inhibition of proapoptotic signals and the promotion of survival signals (L. P. Kane et al., Curr. Biol. 9:601–604, 1999; G. J. Kops et al., Nature 398:630–634, 1999). Evidence supporting the importance of the PI3K/Akt signaling pathway in tumorigenesis stems from experiments with transgenic mice bearing polyomavirus middle T antigen under the control of the mouse mammary tumor virus long terminal repeat promoter. Mammary epithelium-specific expression of polyomavirus middle T antigen results in the rapid development of multifocal metastatic mammary tumors, whereas transgenic mice expressing a mutant middle T antigen decoupled from the phosphatidylinositol 3′-OH kinase (MTY315/322F) develop extensive mammary gland hyperplasias that are highly apoptotic. To directly assess the role of Akt in mammary epithelial development and tumorigenesis, we generated transgenic mice expressing constitutively active Akt (HAPKB308D473D or Akt-DD). Although expression of Akt-DD interferes with normal mammary gland involution, tumors were not observed in these strains. However, coexpression of Akt-DD with MTY315/322F resulted in a dramatic acceleration of mammary tumorigenesis correlated with reduced apoptotic cell death. Furthermore, coexpression of Akt-DD with MTY315/322F resulted in phosphorylation of the FKHR forkhead transcription factor and translational upregulation of cyclin D1 levels. Importantly, we did not observe an associated restoration of wild-type metastasis levels in the bitransgenic strain. Taken together these observations indicate that activation of Akt can contribute to tumor progression by providing an important cell survival signal but does not promote metastatic progression.