Miracle-dz/UniFAR-FTUs huggingface dataset:
PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes

Peroxisomes are membrane-bound organelles within eukaryotic cells that post-translationally import folded proteins into their matrix. Matrix protein import requires a shuttle receptor protein, usually PEX5, that cycles through docking with the peroxisomal membrane, ubiquitination, and export back into the cytosol followed by deubiquitination. Matrix proteins associate with PEX5 in the cytosol and are translocated into the peroxisome lumen during the PEX5 cycle. This cargo translocation step is not well understood, and its energetics remain controversial. We use stochastic computational models to explore different ways the AAA ATPase driven removal of PEX5 may couple with cargo translocation in peroxisomal importers of mammalian cells. The first model considered is uncoupled, in which translocation is spontaneous, and does not immediately depend on PEX5 removal. The second is directly coupled, in which cargo translocation only occurs when its PEX5 is removed from the peroxisomal membrane. The third, novel, model is cooperatively coupled and requires two PEX5 on a given importomer for cargo translocation — one PEX5 with associated cargo and one with ubiquitin. We measure both the PEX5 and the ubiquitin levels on the peroxisomes as we vary the matrix protein cargo addition rate into the cytosol. We find that both uncoupled and directly coupled translocation behave identically with respect to PEX5 and ubiquitin, and the peroxisomal ubiquitin signal increases as the matrix protein traffic increases. In contrast, cooperatively coupled translocation behaves dramatically differently, with a ubiquitin signal that decreases with increasing matrix protein traffic. Recent work has shown that ubiquitin on mammalian peroxisome membranes can lead to selective degradation by autophagy, or ‘pexophagy. ’ Therefore, the high ubiquitin level for low matrix cargo traffic with cooperatively coupled protein translocation could be used as a disuse signal to mediate pexophagy. This mechanism may be one way that cells could regulate peroxisome numbers.
A System for Measuring Tremor Intensity in Rats

An accurate and physically defined system for measuring tremor in unanesthetized and unrestrained rats is described. The method is based on measuring the vibrations of an ordinary animal cage induced by the tremor of the animal inside it. The vibrations of the animal cage were recorded with a piezoelectric acceleration sensor and analyzed using a microprocessor on-line system. The computer was programmed in assembly language to perform a fast Fourier transform (FFT) spectrum analysis in real time. In those cases in which a frequency distribution curve is too complicated to handle, a mean value of all tremor components belonging to the different frequencies can be used. This mean value is called tremor intensity. Theoretical considerations using the spectral density distribution were employed to find a physically motivated measure of tremor intensity. The measuring system is carefully analyzed, and it is shown that the output of the system can be adjusted to give an estimate of the theoretically motivated measure of the tremor intensity. Measurements of some drug-induced tremor spectra are represented.
Activation of mitogen‐activated protein kinases via CD40 is distinct from that stimulated by surface IgM on B cells

CD40 plays critical roles in B cell proliferation and differentiation in response to T cell‐dependent antigenic stimulation. It has been suggested that CD40‐mediated biological activities are transduced by a CD40 receptor‐associated factor, CRAF1 and probably by protein tyrosine kinase Lyn and its substrates, phospholipase Cγ (PLCγ) and phosphatidylinositol‐3 kinase (PI‐3 kinase). Here, we describe the novel finding that a mitogen‐activated protein kinase (MAPK)/extracellular signal‐regulated protein kinase (ERK) cascade is involved in CD40 signaling in mouse B cells. Analysis of ERK activities in the B cell lymphoma cell line WEHI 231, which shows an increase in DNA synthesis or arrest of the cell cycle by cross‐linking of CD40 or surface IgM (sIgM) cross‐linking, respectively, indicated that one of the ERK isoforms, ERK2, was preferentially and rapidly activated after CD40 cross‐linking. The CD40‐mediated ERK2 activation was comparable to that after sIgM stimulation, although the activity was reduced toward the basal level within several minutes after stimulation. In contrast, ERK1 and ERK2 were activated to a similar extent by sIgM cross‐linking, and the activities remained stable for at least 10 min. Furthermore, similar features of differential activation of ERK isoforms were observed in normal resting B cells in CD40 and sIgM signaling. These results suggest divergent regulatory pathways for ERK1 and ERK2 activation, and they support the notion that CD40 signaling may utilize a limited set of elements in the ERK cascade. Co‐stimulation of WEHI 231 cells with anti‐CD40 mAb rescues the cells from anti‐IgM‐mediated apoptosis, whereas this co‐stimulation resulted in activation of ERK isoforms comparable to that in sIgM stimulation, without a synergistic effect. This result indicates the dominance of ERK activation in sIgM signaling over that of CD40, and it suggests that ERK activation may not be linked to the biological effect that CD40 stimulation in this cell line.
Relaciones entre profesionales de la salud y usuarios/as desde la perspectiva de género

The objective of this article is to analyze relationships between health professionals and users from a gender perspective. Using Pierre Bourdieu as a theoretical reference, we critically analyze data from two studies carried out in Brazil in which we took part as authors. The first of these studies was based in Rio de Janeiro and the second was a multicenter and ethnographical study carried out in eight health care facilities distributed throughout four Brazilian states, two in the Southeast region and two in the Northeast region. Among the principal results of the present study, we found that although the relationships between health professionals and users demonstrate varied opinions, all are marked by a gendered habitus. We conclude that, among other aspects, the construction of diverse femininities and masculinities and the way in which these are exercised in health care contexts are the product of process that is both socio-historical and personal.
Interactive Data Mining and Visualization

Interactive analysis introduces dynamic changes in Visualization. On another hand, advanced visualization can provide different perspectives of the data to the user, hence, provide effective way of data mining. This paper discusses new ideas for interactive data mining tool based on R through HCI techniques. Also demonstrates the purposed features through data mining and visualization examples, such as ensemble method and tree map. Lastly, explore some possibilities and difficulties from the view of implement. Because of the fast rate of increasing in data complexity, existing efficiency of data mining is facing great challenge. There are emerging different data mining languages and related tool set. R language is one of the popular languages, which is specially welcomed by scientists and other professionals in education. They have accumulated thousands of data mining packages for different algorithms and also a lot of examples are available. It’s very helpful for coming researchers and novice learners like us to focus on R language and related packages currently. However, current data analysis tools for R like R-Studio simply integrate some visualization tool without considering the significance of human interactions. Traditional machine learning techniques don’t emphasize the user’s involvement. Such tools tend to rely on statistical analysis and plotting, and are not open enough to combine other cutting edge visualization techniques in time. Other commercial statistic analysis software like SPSS without openness is also not fit for our research purpose. To implement effective interactive data mining, this paper discusses a new idea and proposes for data mining tool combining human computer interaction techniques based on new visualization methods.
Melatonin in Alzheimer’s Disease

Alzheimer’s disease (AD), an age-related neurodegenerative disorder with progressive cognition deficit, is characterized by extracellular senile plaques (SP) of aggregated β-amyloid (Aβ) and intracellular neurofibrillary tangles, mainly containing the hyperphosphorylated microtubule-associated protein tau. Multiple factors contribute to the etiology of AD in terms of initiation and progression. Melatonin is an endogenously produced hormone in the brain and decreases during aging and in patients with AD. Data from clinical trials indicate that melatonin supplementation improves sleep, ameliorates sundowning and slows down the progression of cognitive impairment in AD patients. Melatonin efficiently protects neuronal cells from Aβ-mediated toxicity via antioxidant and anti-amyloid properties. It not only inhibits Aβ generation, but also arrests the formation of amyloid fibrils by a structure-dependent interaction with Aβ. Our studies have demonstrated that melatonin efficiently attenuates Alzheimer-like tau hyperphosphorylation. Although the exact mechanism is still not fully understood, a direct regulatory influence of melatonin on the activities of protein kinases and protein phosphatases is proposed. Additionally, melatonin also plays a role in protecting the cholinergic system and in anti-inflammation. The aim of this review is to stimulate interest in melatonin as a potentially useful agent in the prevention and treatment of AD.
Direct fitting of center collinear circles for equidistant fish-eye camera calibration

Abstract. An equidistant fish-eye camera can be calibrated using a single image of two sets of parallel lines in the scene, which is very convenient for practical applications. The core of the calibration procedure is the fitting of center collinear circles that intersect at two vanishing points. A fast and accurate fitting method that can be used for equidistant fish-eye camera calibration is presented. First, the fitting problem is formulated as a nonlinear least square problem and solved using Levenberg-Marquardt optimization. The objective function is also derived, as well as the Jacobian required by the Levenberg-Marquardt algorithm. It is also demonstrated how to determine the initial estimations. Experimental results on synthetic data have demonstrated the superiority of our method to two existing approaches in terms of speed and accuracy. Results on real data have also demonstrated its effectiveness for fish-eye camera calibration.
TTI-COIN at SemEval-2017 Task 10: Investigating Embeddings for End-to-End Relation Extraction from Scientific Papers

This paper describes our TTI-COIN system that participated in SemEval-2017 Task 10. We investigated appropriate embeddings to adapt a neural end-to-end entity and relation extraction system LSTM-ER to this task. We participated in the full task setting of the entity segmentation, entity classification and relation classification (scenario 1) and the setting of relation classification only (scenario 3). The system was directly applied to the scenario 1 without modifying the codes thanks to its generality and flexibility. Our evaluation results show that the choice of appropriate pre-trained embeddings affected the performance significantly. With the best embeddings, our system was ranked third in the scenario 1 with the micro F1 score of 0.38. We also confirm that our system can produce the micro F1 score of 0.48 for the scenario 3 on the test data, and this score is close to the score of the 3rd ranked system in the task.
Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.
Shape-based Image Correspondence

Current state-of-the-art dense correspondence algorithms establish correspondences between pair of images by searching for a flow field that minimizes the distance between local signatures (e.g., color histogram, SIFT descriptor) of aligned pixels while preserving smoothness. Agnostic to the global signatures (e.g., object membership, category of object), these local signatures face difficulties in resolving alignment ambiguities when scene content undergoes type and configuration variation. In this paper, we investigate the effect of adding shape correspondence constraints either in the form of pair of corresponding contour fragments or pair of closed curves. We find the shape does not play a significant role in optical flow and stereo correspondence but it does play a significant role when scene content changes are large. We also explore using object proposals as a way of providing shape constraints with encouraging results.
The Wedding Dress

The Wedding Dress presents an epiphanous shift in a couple's understanding of exogamy and commitment when confronted with extended family's clannish expectations. Submitting to and then challenging and destroying this power's hold is symbolized in the wedding dress. As an autoethnography, this story resonates with Sophocles's Antigone, in which choices must be made that challenge the law of the father (King Kreon, Jane-family) and demand the law of nature (marriage rights) to prevail. In Antigone, Kreon's son Heron is engaged to Antigone, who challenges the king's unnatural edict to leave a warrior's body unburied. In the end, Heron chooses Antigone over his father and dies with his fiancé in a tomb—thus shattering the laws of humans while upholding the laws of nature. A story of survival, a fight for autonomy, The Wedding Dress captures marital tensions that arise from forced choices and the triumph of facing them truthfully together.
Efficient test-based model generation for legacy reactive systems

We present the effects of using an efficient algorithm for behavior-based model synthesis which is specifically tailored to reactive (legacy) system behaviors. Conceptual backbone is the classical automata learning procedure L*, which we adapt according to the considered application profile. The resulting learning procedure L*Meal , which directly synthesizes generalized Mealy automata from behavioral observations gathered via an automated test environment, drastically outperforms the classical learning algorithm for deterministic finite automata. Thus it marks a milestone towards opening industrial legacy systems to model-based test suite enhancement, test coverage analysis, and online testing.
Half Full or Half Empty

Previous research demonstrates the dysfunctional consequences of high levels of role stressors (role ambiguity and role conflict) in boundary-spanning positions. These consequences include higher levels of burnout and lower levels of satisfaction and performance. Although marketing researchers have investigated external mechanisms for coping with role stressors, research to date has not investigated the inherent capability of boundary spanners to cope with role stressors. This research examines optimism as an internal characteristic that facilitates coping with role stressors in boundary-spanning positions. The research findings reveal that optimists are able to anticipate and respond proactively to stressors, resulting in less burnout and higher levels of performance and satisfaction.
Student Perceptions of "Better Readers" in Elementary Classrooms

The Elementary School Journal Volume 82, Number 5 ? 1982 by The University of Chicago. All rights reserved. 0013-5984/82/8205-0002$01.00 In elementary school, students learn to compare and evaluate the performances of their peers and of themselves. The very nature of the schooling experience may be responsible for this fact. When they enter school, students enter an environment where many students of the same age work together in the same room on the same or similar tasks, where there are general expectations for how quickly students will progress, and where achievement is rewarded. In this environment students
Selbstkonzept nach erworbenen Hirnschädigungen: Veränderungen der Selbstwahrnehmung und Subjektives Wohlbefinden

Negative self-concepts relate to increased depressive symptoms and psychosocial burden and reduced quality of life, which underlines their importance in rehabilitation processes. Changes in self-concept in 59 inpatients and 29 post-acute outpatients with acquired brain injury were examined. Compared to premorbid appraisals, both samples evaluate post-injury self-concepts more negatively. Factor analysis reveals 2 self-concept domains ("emotional experience", "social interaction characteristics"), which are impacted differentially by the injury. Negative post- injury self-concepts are strongly linked to reduced subjective well-being and explain a substantial amount of variance in subjective well- being in multiple regression models. Sociodemographic and injury-related variables play a secondary role. These findings speak in favour of considering interventions aiming at improvement of self-concept in psychotherapeutic counselling after acquired brain injury.
Linking Childhood Exposure to Physical Abuse and Adult Offending: Examining Mediating Factors and Gendered Relationships

This article examines relationships between physical abuse and official and self‐reported offending among 480 male and female offenders serving community corrections orders in Queensland, Australia. It examines whether offending rates vary between abused and non‐abused respondents and whether the abuse–offending relationship is maintained in the presence of demographic and juvenile offending variables. The study explores whether family and school factors can mediate the abuse–offending relationship. The results reveal that physically abused offenders reported higher rates of violent, property, and total offending than non‐abused offenders. The effects of abuse on violent and property crime were reduced with the introduction of demographic and juvenile offending variables, but an overall effect of physical abuse remained for total offending. Maternal support was associated with lower levels of adult offending among physically abused respondents, while school expulsion and attachment to school for non‐conventional reasons (e.g., non‐academic) appeared to exacerbate the abuse–offending relationship.
The effects of children’s reading skills and interest on teacher perceptions of children’s skills and individualized support

This study examined the effects of children’s reading skills and interest in reading-related tasks on teacher perceptions of children’s literacy skills (reading and spelling) and the respective individualized support for children during the first two years of formal schooling. The participants were 334 children and their classroom teachers. Identical measures were administered at three time points (at the beginning of Grade 1 and at the end of Grades 1 and 2). Children’s reading skills were assessed with the word reading fluency test, and their interest in reading was assessed with self-reports. Also, teachers evaluated each child’s level of reading and spelling skills and reported the level of individual literacy support they provided. The results showed that children’s poor skills in reading at the beginning of Grade 1 were related to both teacher perceptions of children’s skills as being poor and to increased support at the end of Grade 1. In turn, teacher perceptions of children’s skills as being poor at the end of Grade 1 were related to more support at the end of Grade 2. Moreover, children’s reading skills at the beginning of school had an indirect effect via teacher perceptions at the end of Grade 1 on teacher support in Grade 2. The findings underscore the importance of examining the role of teacher perceptions in providing individualized support during literacy activities.
ACTION FAILURE RECOVERY VIA MODEL‐BASED DIAGNOSIS AND CONFORMANT PLANNING

A plan carried on in the real world may be affected by a number of unexpected events, plan threats, which cause significant deviations between the intended behavior of the plan executor (i.e., the agent) and the observed one. These deviations are typically considered as action failures. This paper addresses the problem of recovering from action failures caused by a specific class of plan threats: faults in the functionalities of the agent. The problem is approached by exploiting techniques of the Model‐Based Diagnosis (MBD) for detecting failures (plan execution monitoring) and for explaining these failures in terms of faulty functionalities (agent diagnosis). The recovery process is modeled as a replanning problem aimed at fixing the faulty components identified by the agent diagnosis. However, since the diagnosis is in general ambiguous (a failure may be explained by alternative faults), the recovery has to deal with such an uncertainty. The paper advocates the adoption of a conformant planner, which guarantees that the recovery plan, if it exists, is executable no matter what the actual cause of the failure. The paper focuses on a single agent performing its own plan, however the proposed methodology takes also into account that agents are typically situated into a multiagent scenario and that commitments between agents may exist. The repair strategy is therefore conceived to overcome the causes of a failure while assuring the commitments an agent has agreed with other team members.
Organizational Control Structure and Member Consensus

The relationships between varying patterns of organizational control and member consensus were investigated in thirty-two geographically separate units of a nationally organized delivery company. The hypotheses predicted that high rank-and-file control relative to that of upper echelons and a high amount of control exercised by members at all echelons would be positively associated with member consensus. The results fail to confirm the first hypothesis. The second hypothesis is supported-a high amount of total control is positively associated with both work-group consensus and hierarchical consensus. The results were seen as part of a larger organizational power syndrome.