Miracle-dz/UniFAR-FTUs huggingface dataset:
Binding characteristics of galectin-3 fusion proteins

Galectin-3 modulates cell adhesion and signaling events by specific binding and cross-linking galactoside containing carbohydrate ligands. Proteolytic cleavage by metalloproteinases yields in vivo N-terminally truncated galectin-3 still bearing the carbohydrate recognition domain. Truncated galectin-3 has been demonstrated to act in vivo as a negative inhibitor of galectin-3 due to higher affinity for carbohydrate ligands. We here present our studies on a series of 12 human galectin-3 protein constructs. Truncated galectin-3 (∆1-62 and ∆1-116) and fusions with SNAP-tag and/or yellow fluorescent protein (YFP) display altered binding efficiencies (ratio of maximum binding signal and apparent affinity constant Kd) to asialofetuin (ASF) in solid-phase enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR) binding assays. Galectin-3(Δ1-62) and full-length (native) galectin-3 have highest affinity to ASF in ELISA and SPR experiments, respectively, whereas galectin-3(Δ1-116) shows only weak binding. We demonstrate here for the first time that SNAP-tag and YFP fusions of galectin-3 and truncated galectin-3 proteins improve binding efficiencies to ASF. SNAP-tagged galectin-3, galectin-3(Δ1-62) and galectin-3(Δ1-116) are found with significant (3- to 6-fold) higher binding efficiencies in SPR when compared with native galectin-3. Fusion of truncated galectin-3 with YFP renders binding properties similar to native galectin-3, whereas in combination with SNAP-tag improved binding characteristics are obtained. Our results emphasize the importance of the N-terminal domain of human galectin-3 for ligand binding. Most importantly, in combination with fusion proteins suitable for the design of diagnostic and therapeutic tools binding properties can be beneficially tuned. The resulting novel protein tools may be advantageous for potential galectin-3 directed applications in tumor diagnostics and therapy.
Challenging lives: an exploratory qualitative study of quality of life in young adults living with a chronic neurological condition

Abstract Objectives: The transition from adolescence to young adulthood is traditionally a time of self-discovery, career establishment, and the development of relationships. However, for young adults with a chronic illness this time in life can be very challenging, and the management of the transition is crucial for these young adults to reach their potential. The purpose of this study was to explore the lived experiences, perceptions, and challenges of young adults with a chronic neurological condition undergoing the transition from adolescence to adulthood. The Quality of Life model was used to inform the interview schedule and explored two specific areas: identity and condition. Methods: Six participants with chronic neurological conditions (age 18–25 years) took part in the study. Audio-recorded semi-structured interviews were transcribed verbatim and analyzed using Interpretive Phenomenological Analysis. Results: The findings revealed a number of interlinking superordinate themes across the participants: ‘condition’, ‘support’, ‘strive for independence’, and ‘transition’. Conclusions: The findings of this exploratory study provide a visible indication of the specific needs of the participant group, including informational and social support needs, and removal of barriers for successful participation. They also highlight holistic service requirements and the interlinking relationships of the direction of support which could be provided to meet these needs.
Brain Based Control of Wheelchair

This paper presents a brain based control of the wheelchair for physically impaired users. The design of the system is focused on receiving electroencephalographic (EEG) signals from the brain, processing and turning the system and then performing control of the wheelchair. The number of experimental measurements of brain activity has been obtained using human control commands of the wheelchair. The obtained data including EEG signals and control commands are used to design brain based control mechanism in training mode. The classification of brain signals has been done using a Support Vector Machine (SVM) and neural networks. The training data is used before using the system under real conditions. Then test data is applied to measure the accuracy of the control. The system designed in this paper is adjusted to control a wheelchair with five commands: move forward, move backward, stop, turn left and turn right in real conditions. The provided approach allows reducing the probability of misclassification and improving control accuracy of the wheelchair.
Impact on Length of Stay After Introduction of Emergency Department Information System

Objective: An electronic emergency department information system (EDIS) can monitor the progress of a patient visit, facilitate computerized physician order entry, display test results and generate an electronic medical record. Ideally, use of an EDIS will increase overall emergency department (ED) efficiency. However, in academic settings where new interns rotate through the ED monthly, the “learning curve” experienced by the new EDIS user may slow down patient care. In this study, we measured the impact of the “intern learning curve” on patient length of stay (LOS). Methods: We retrospectively analyzed one year of patient care data, generated by a comprehensive EDIS in a single, urban, university-affiliated ED. Intern rotations began on the 23rd of each month and ended on the 22nd of the next month. Interns received a 1.5-hour orientation to the EDIS prior to starting their rotation; none had prior experience using the electronic system. Mean LOS (± standard error of the mean) for all patients treated by an intern were calculated for each day of the month. Values for similar numerical days from each month were combined and averaged over the year resulting in 31 discrete mean LOS values. The mean LOS on the first day of the intern rotation was compared with the mean LOS on the last day, using Student’s t-test. Results: During the study period 9,780 patients were cared for by interns; of these, 7,616 (78%) were discharged from the ED and 2,164 (22%) were admitted to the hospital. The mean LOS for all patients on all days was 267 ± 1.8 minutes. There was no difference between the LOS on the first day of the rotation (263±9 minutes) and the last day of the rotation (276 ± 11 minutes, p > 0.9). In a multiple linear regression model, the day of the intern rotation was not associated with patient LOS, even after adjusting for the number of patients treated by interns and total ED census (β = −0.34, p = 0.11). Conclusion: In this academic ED, where there is complete intern “turnover” every month, there was no discernible impact of the EDIS “learning curve” on patient LOS.
Preliminary results on globally asymptotically stable simultaneous localization and mapping in 3-D

This paper presents the design, analysis, performance evaluation, and preliminary experimental validation of a globally asymptotically stable (GAS) filter for simultaneous localization and mapping (SLAM) with application to unmanned aerial vehicles (UAVs). The SLAM problem is formulated in a sensor-based framework and modified in such a way that the system structure may be regarded as linear time-varying for observability purposes, from which a Kalman filter with GAS error dynamics follows naturally. The proposed solution includes the estimation of both body-fixed linear velocity and rate-gyro measurement biases. Both simulation results and preliminary experimental results, using an instrumented quadrotor equipped with a RGB-D camera, are included in the paper to illustrate the performance of the algorithm under realistic conditions.
Fine-grained parallel XML filtering for content-based publish/subscribe systems

Current XML-based publish/subscribe systems only support coarse-grained message filtering: a message is either forwarded to a subscriber in its entirety or not at all. Fine-grained filtering of message elements is not supported. Such filtering capabilities can be used by subscribers to further detail their subscriptions or by message brokers to enforce fine-grained access control policies. This paper presents an XML filtering engine that enables fine-grained, parallel filtering of XML streams. It uses a novel subscription model based on the concept of nested filters and supports the efficient evaluation of constraints on node sets. We detail the data structures and algorithms used by the system to evaluate filters while parsing an XML stream and to reconstruct client-specific message versions. Experimental results show that the system can efficiently handle thousands of subscriptions and scales well with the number of active parallel filtering threads.
Cross-lingual genre classification for closely related languages

— Resource-scarcity is a topic that is continually researched by the HLT community, especially for the South-African context. We explore the possibility of leveraging existing resources to help facilitate the development of new resources for under-resourced languages by using cross-lingual classification methods. We investigate the application of an Afrikaans genre classification system on Dutch texts and see encouraging results of 63.1% when classifying raw Dutch texts. We attempt to optimise the performance by employing a machine translation pre-processing step, boosting performance of the Afrikaans system on Dutch data to 67.2%. Further investigation is required as we conclude that the robustness of the Afrikaans genre classification system needs improvement.
Toward standardization of carbohydrate-deficient transferrin (CDT) measurements: II. Performance of a laboratory network running the HPLC candidate reference measurement procedure and evaluation of a candidate reference material

Abstract Carbohydrate-deficient transferrin (CDT) is a descriptive term used for a temporary change in the transferrin glycosylation profile caused by alcohol, and used as a biomarker of chronic high alcohol consumption. The use of an array of methods for measurement of CDT in various absolute or relative amounts, and sometimes covering different transferrin glycoforms, has complicated the comparability of results and caused confusion among medical staff. This situation prompted initiation of an IFCC Working Group on CDT standardization. This second publication of the WG-CDT covers the establishment of a network of reference laboratories running a high-performance liquid chromatography (HPLC) candidate reference measurement procedure, and evaluation of candidate secondary reference materials. The network laboratories demonstrated good and reproducible performance and thus can be used to assign target values for calibrators and controls. A candidate secondary reference material based on native human serum lyophilized with a cryo-/lyoprotectant to prevent protein denaturation was found to be commutable and stable during storage. A proposed strategy for calibration of different CDT methods is also presented. In an external quality assurance study involving 66 laboratories and covering the current routine CDT assays (HPLC, capillary electrophoresis and immunoassay), recalculation of observed results based on the nominal values for the candidate calibrator reduced the overall coefficient of variation from 18.9% to 5.5%. The logistics for distribution of reference materials and review of results were found to be functional, indicating that a full reference system for CDT may soon be available. Clin Chem Lab Med 2010;48:1585–92.
Arenogigas armoricus, a New Genus and Species of a Monostiliferous Hoplonemertean (Nemertea) from the North-West Coast of France

A new genus and species of an endobenthic, unusually large eumonostiliferous hoplonemertean, Arenogigas armoricus gen. et sp. nov., is described from an intertidal sandflat in Pouldohan Bay near Concarneau, France. Morphological characters of the species and genus include a prominent connective tissue that divides the anterior longitudinal musculature, an extremely branched vascular system, the absence of a pre-cerebral septum, a pair of eyes situated at the anterior tip of the head, small cerebral organs positioned far anterior to the brain, 10 proboscidial nerves, and nine accessory stylet pouches.
Aldosterone mediates angiotensin II‐induced interstitial cardiac fibrosis via a Nox2‐containing NADPH oxidase

Angiotensin (ANG) II (AngII) and aldosterone contribute to the development of interstitial cardiac fibrosis. We investigated the potential role of a Nox2‐containing NADPH oxidase in aldosterone‐induced fibrosis and the involvement of this mechanism in AngII‐induced effects. Nox2−/− mice were compared with matched wild‐type controls (WT). In WT mice, subcutaneous (s.c.) AngII (1.1 mg/kg/day for 2 wk) significantly increased NADPH oxidase activity, interstitial fibrosis (11.5±1.0% vs. 7.2±0.7%; P<0.05), expression of fibronectin, procollagen I, and connective tissue growth factor mRNA, MMP‐2 activity, and NF‐kB activation. These effects were all inhibited in Nox2−/− hearts. The mineralocorticoid receptor antagonist spironolactone inhibited AngII‐induced increases in NADPH oxidase activity and the increase in interstitial fibrosis. In a model of mineralocorticoid‐dependent hypertension involving chronic aldosterone infusion (0.2 mg/kg/day) and a 1% Na Cl diet (“ALDO”), WT animals exhibited increased NADPH oxidase activity, pro‐fibrotic gene expression, MMP‐2 activity, NF‐kB activation, and significant interstitial cardiac fibrosis (12.0±1.7% with ALDO vs. 6.3±0.3% without; P<0.05). These effects were inhibited in Nox2−/− ALDO mice (e.g., fibrosis 6.8±0.8% with ALDO vs. 5.8±1.0% without ALDO; P=NS). These results suggest that aldosterone‐dependent activation of a Nox2‐containing NADPH oxidase contributes to the profibrotic effect of AngII in the heart as well as the fibrosis seen in mineralocorticoid‐dependent hypertension. —Johar, S. , Cave, A. C. , Narayanapanicker, A. , Grieve, D. J., Shah, A. M. Aldosterone mediates angiotensin II‐induced interstitial cardiac fibrosis via a Nox2‐containing NADPH oxidase. FASEB J. 20, E846–E854 (2006)
A Heuristic Scheduling of Independent Tasks with Bottleneck Resource Constraints

In this paper, the problem of scheduling independent tasks with bottleneck resource constraints is investigated. There is a set of independent tasks ${\cal T} = \{T_1, \ldots, T_n\}$ and a set of resources ${\cal R} = \{R_1, \ldots, R_m\}$. The available amount of resource $R_j$, for $j = 1, \ldots, m$, is (normalized to) 1. Each task $T_i$'s execution requires at least $\lambda_{(i,j)} \leq 1$ units of resource $R_j \in {\cal R}$, and with these minimal resources, the execution time of $T_i$ is $\tau_i$. If there is a resource $R_{\beta(i)}$ so that $T_i$ can use $\xi$ units $(\xi \geq \lambda_{(i, \beta(j))})$ and reduce the execution time to $\frac{\lambda_{(i, \beta(i))}}{\xi} \tau_{i}$, we say that $T_i$ can achieve linear speed-up with respect to $R_{\beta(i)}$. It is assumed that for each $T_i$, there is one, and only one, resource $R_{\beta(i)}$ that is $T_i$'s bottleneck resource: $T_i$ can use $\xi$ units of $R_{(i, \beta(i))}$ and achieve linear speed-up, where $\xi$ is between $\lambda_{(i, \beta(i))}$ and $\Lambda_{(i, \beta(i))} \leq 1$. The problem is to find a feasible schedule for all the tasks in ${\cal T}$ that has a shortest overall makespan. This problem is a combination of two previously studied problems---scheduling tasks with resource constraints [SIAM J. Comput. , 4 (1975), pp.~187--200. ] scheduling parallel tasks [SIAM J. Comput. , 21 (1992), pp.~281--294]. A variant of this problem was studied in [J. Combin. Theory, 21 (1976), pp.~257--298]. Because the problem is NP-hard, we propose the ECT (earliest completion time) algorithm as a heuristic solution and show that the performance ratio of the ECT makespan $M_{{\scriptsize ECT}}$ to the optimal makespan $M_{{\scriptsize OPT}}$ is bounded by $2l+m+1$, where $l$ is the number of the bottleneck resources in ${\cal R}$. When $l=0$, this is exactly the performance bound shown by Garey and Graham in [SIAM J. Comput. , 4 (1975), pp.~187--200].
Stemming versus Light Stemming for measuring the simitilarity between Arabic Words with Latent Semantic Analysis model

Representation of semantic information contained in the words is needed for any Arabic Text Mining applications. More precisely, the purpose is to better take into account the semantic dependencies between words expressed by the co-occurrence frequencies of these words. There have been many proposals to compute similarities between words based on their distributions in contexts. In this paper, we compare and contrast the effect of two preprocessing techniques applied to Arabic corpus: Stemming, and Light Stemming techniques for measuring the semantic between Arabic words with the well known abstractive model -Latent Semantic Analysis (LSA)- with a wide variety of distance functions and similarity measures, such as the Euclidean Distance, Cosine Similarity, Jaccard Coefficient, and the Pearson Correlation Coefficient. The obtained results show that, on the one hand, the variety of the corpus produces more accurate results; on the other hand, the Light Stemming outperformed the Stemming approach because Stemming affects the words meanings.
A genealogy of hacking

Hacking is now a widely discussed and known phenomenon, but remains difficult to define and empirically identify because it has come to refer to many different, sometimes incompatible, material practices. This article proposes genealogy as a framework for understanding hacking by briefly revisiting Foucault’s concept of genealogy and interpreting its perspectival stance through the feminist materialist concept of the situated observer. Using genealogy as a theoretical frame, a history of hacking will be proposed in four phases. The first phase is the ‘prehistory’ of hacking in which four core practices were developed. The second phase is the ‘golden age of cracking’ in which hacking becomes a self-conscious identity and community and is for many identified with breaking into computers, even while non-cracking practices such as free software mature. The third phase sees hacking divide into a number of new practices even while old practices continue, including the rise of serious cybercrime, hacktivism, the division of Open Source and Free Software and hacking as an ethic of business and work. The final phase sees broad consciousness of state-sponsored hacking, the re-rise of hardware hacking in maker labs and hack spaces and the diffusion of hacking into a broad ‘clever’ practice. In conclusion, it will be argued that hacking consists across all the practices surveyed of an interrogation of the rationality of information technocultures enacted by each hacker practice situating itself within a particular technoculture and then using that technoculture to change itself, both in changing potential actions that can be taken and changing the nature of the technoculture itself.
Syntactic simplification for machine translation

This paper presents a new rule-based Syntactic Simplification system for the Spanish language. The system basically consists of splitting complex sentences into several simple ones preserving its original meaning. It is envisioned to be a preprocessing tool for other Natural Language Processing applications such as Text Summarization, Information Extraction, Parsing and Machine Translation. According to the evaluation, the application of the syntactic rules proposed clearly improves Machine Translation from Spanish to far target languages such as Korean and Chinese. A parallel corpus of Spanish original and simplified texts has been manually built and validated by native Spanish speakers for this research. In addition, an experiment was carried out among two groups of Spanish learners comparing their reading comprehension of original and simplified texts. Their answers show a null correlation between simplification and text comprehension. The automatic Syntactic Simplification system has also been intrinsically evaluated obtaining promising results.
Meaning Constructs and Meaning-Oriented Techniques: Clinical Applications of Meaning and Existential Exploration

Meaning is a universal concept, yet it does not have a universal, agreed upon definition among the clinical literature. Although all human beings are pulled toward being able to uncover, discover, maintain, and enhance meaning in life, despite difficult aspects of the human condition, we are faced with the task of understanding a person's meaning construct in any given circumstance. A “meaning construct model” is explored as a way of understanding how human beings define and develop meaning constructs. Additionally, clinical interventions of meaning-centered logotherapy and existential analysis, (a therapy with meaning as its central process) are expounded on to offer concrete methods of discovering and enhancing meaning in life, and for an exploration of existence.
Accept–reject Metropolis–Hastings sampling and marginal likelihood estimation

We describe a method for estimating the marginal likelihood, based on Chib (1995) and Chib and Jeliazkov (2001) , when simulation from the posterior distribution of the model parameters is by the accept–reject Metropolis–Hastings (ARMH) algorithm. The method is developed for one‐block and multiple‐block ARMH algorithms and does not require the (typically) unknown normalizing constant of the proposal density. The problem of calculating the numerical standard error of the estimates is also considered and a procedure based on batch means is developed. Two examples, dealing with a multinomial logit model and a Gaussian regression model with non‐conjugate priors, are provided to illustrate the efficiency and applicability of the method.
Childhood Trauma and PTSD Symptoms Increase the Risk of Cognitive Impairment in a Sample of Former Indentured Child Laborers in Old Age

A growing body of evidence suggests a link between early childhood trauma, post-traumatic stress disorder (PTSD) and higher risk for dementia in old age. The aim of the present study was to investigate the association between childhood trauma exposure, PTSD and neurocognitive function in a unique cohort of former indentured Swiss child laborers in their late adulthood. To the best of our knowledge this is the first study ever conducted on former indentured child laborers and the first to investigate the relationship between childhood versus adulthood trauma and cognitive function. According to PTSD symptoms and whether they experienced childhood trauma (CT) or adulthood trauma (AT), participants (n = 96) were categorized as belonging to one of four groups: CT/PTSD+, CT/PTSD-, AT/PTSD+, AT/PTSD-. Information on cognitive function was assessed using the Structured Interview for Diagnosis of Dementia of Alzheimer Type, Multi-infarct Dementia and Dementia of other Etiology according to ICD-10 and DSM-III-R, the Mini-Mental State Examination, and a vocabulary test. Depressive symptoms were investigated as a potential mediator for neurocognitive functioning. Individuals screening positively for PTSD symptoms performed worse on all cognitive tasks compared to healthy individuals, independent of whether they reported childhood or adulthood adversity. When controlling for depressive symptoms, the relationship between PTSD symptoms and poor cognitive function became stronger. Overall, results tentatively indicate that PTSD is accompanied by cognitive deficits which appear to be independent of earlier childhood adversity. Our findings suggest that cognitive deficits in old age may be partly a consequence of PTSD or at least be aggravated by it. However, several study limitations need to considered. Consideration of cognitive deficits when treating PTSD patients and victims of lifespan trauma (even without a diagnosis of a psychiatric condition) is crucial. Furthermore, early intervention may prevent long-term deficits in memory function and development of dementia in adulthood.