Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid and persistent impairments of the forelimb motor representations following cervical deafferentation in rats

Skilled motor control is regulated by the convergence of somatic sensory and motor signals in brain and spinal motor circuits. Cervical deafferentation is known to diminish forelimb somatic sensory representations rapidly and to impair forelimb movements. Our focus was to determine what effect deafferentation has on the motor representations in motor cortex, knowledge of which could provide new insights into the locus of impairment following somatic sensory loss, such as after spinal cord injury or stroke. We hypothesized that somatic sensory information is important for cortical motor map topography. To investigate this we unilaterally transected the dorsal rootlets in adult rats from C4 to C8 and mapped the forelimb motor representations using intracortical microstimulation, immediately after rhizotomy and following a 2‐week recovery period. Immediately after deafferentation we found that the size of the distal representation was reduced. However, despite this loss of input there were no changes in motor threshold. Two weeks after deafferentation, animals showed a further distal representation reduction, an expansion of the elbow representation, and a small elevation in distal movement threshold. These changes were specific to the forelimb map in the hemisphere contralateral to deafferentation; there were no changes in the hindlimb or intact‐side forelimb representations. Degradation of the contralateral distal forelimb representation probably contributes to the motor control deficits after deafferentation. We propose that somatic sensory inputs are essential for the maintenance of the forelimb motor map in motor cortex and should be considered when rehabilitating patients with peripheral or spinal cord injuries or after stroke.
ProFiDo - The Processes Fitting Toolkit Dortmund

This paper describes the Java-based toolkit ProFiDo which integrates several tools for fitting input models. Currently supported are command line tools for fitting probability distributions, ARIMA processes and Markovian arrival processes. The toolkit provides a graphical user interface which allows for the specification of workflows that describe the different steps of data preprocessing, parameter fitting and result visualization. The basis for the interoperability of the different tools is an XML based interchange format for the specification of various types of processes. An XML based configuration file supports the extension of the toolkit by integrating additional fitting methods or analysis approaches.
Transparent Persistence Appears Problematic for Software Maintenance - A Randomized, Controlled Experiment

Information retrieval from a database is the backbone of many applications. For building object-oriented systems with a relational persistence engine, a common approach is to use an object-to-relational mapping library for handling the mismatch between object-oriented and relational data models. These components should make the application programmer oblivious to the choice of relational database. To study the effects of transparent persistency, we conducted a randomized, controlled study for 16 students, who were given a number of maintenance tasks on a sample software. For half of attendees, the sample software was written using the transparent persistency approach. For the second half the sample software used a self-configuring component for automatically generating database queries. We found out that the group using transparent persistency were performing worse than the group using selfconfigurative queries. Attendees in both groups were using the same amount of time for performing the given maintenance tasks, but the transparent persistency group was outperformed by a factor of three in the number of correct submissions. The use of transparent persistency turned out to be a major error source. This gives us a reason to doubt the usefulness of transparent persistency in the long run.
C-reactive protein, diabetes, and attendance at religious services.

OBJECTIVE Previous studies have shown an association between attendance at religious services and health, particularly cardiovascular morbidity and mortality. People with diabetes have higher risk of cardiovascular mortality and higher C-reactive protein (CRP) levels than people without diabetes. The purpose of this study was to explore the relationship between religious attendance and CRP in people with diabetes. RESEARCH DESIGN AND METHODS This study used cross-sectional survey and examination of a nationally representative sample of noninstitutionalized U.S. adults aged > or = 40 years, derived from the National Health and Nutrition Examination Survey III 1988-1994 (n = 10,059). There were 556 people with diabetes. The primary outcome measure was the presence of elevated CRP. RESULTS There were no differences between people with diabetes compared with people without diabetes in the percentage of those who attended religious services (62.29 vs. 62.0%, P = 0.36). Religious service nonattenders with diabetes were more likely than attenders to have an elevated CRP (odds ratio [OR] 2.17 [95% CI 1.15-4.09]). In people without diabetes, the association between attendance and CRP was not significant (P > 0.05). Among people with diabetes, after adjusting for demographic variables, health status, smoking, social support, mobility, and BMI, the association between religious attendance and CRP remained significant for respondents with diabetes (1.90 [1.03-3.51]). CONCLUSIONS These findings revealed that people with diabetes who have not attended religious services in the previous year are more likely to have elevated levels of CRP. Further research should be conducted to evaluate this association to improve our understanding of the psychological and religious factors that influence diabetes.
Stimulates DNA Synthesis and Cell-Cycle Progression via Its p 55 PIK Regulatory Subunit Interaction with PCNA

Previously, we have shown that p55PIK, an isoform of class IA phosphoinositide 3-kinase (PI3K), specifically interacts with important cell-cycle regulators, such as retinoblastoma (Rb), to promote cellcycle progression. Here, we used the glutathione S-transferase pull-down assay to identify other p55PIKinteracting proteins besides Rb in a Rb-deficient cell line and found that p55PIK interacted with proliferation cell nuclear antigen (PCNA), which plays a key role in coordinating both initiation of the leading strand DNA replication and discontinuous lagging strand synthesis. Overexpression of p55PIK increased, and knockdown decreased, DNA synthesis and DNA replication by modulating the binding of DNA polymerase d (Pold) to PCNA. Moreover, a cell-permeable peptide containing the N-terminal– binding domain of p55PIK (TAT–N24) disrupted the p55PIK–PCNA interaction in cancer cells, and also inhibited the DNA synthesis and tumor growth in cell culture and in vivo. Altogether, our results show that the p55PIK–PCNA interaction is important in regulating DNA synthesis and contributes to tumorigenesis. Furthermore, the p55PIK–PCNA interaction provides a potential new target for anticancer drug development. Mol Cancer Ther; 12(10); 1–10. 2013 AACR.
QUIRE: Lightweight Provenance for Smart Phone Operating Systems

Smartphone apps are often granted to privilege to run with access to the network and sensitive local resources. This makes it difficult for remote endpoints to place any trust in the provenance of network connections originating from a user's device. Even on the phone, different apps with distinct privilege sets can communicate with one another. This can allow one app to trick another into improperly exercising its privileges (resulting in a confused deputy attack). In Quire, we engineered two new security mechanisms into Android to address these issues. First, Quire tracks the call chain of on-device IPCs, allowing an app the choice of operating with the reduced privileges of its callers or exercising its full privilege set by acting explicitly on its own behalf. Second, a lightweight signature scheme allows any app to create a signed statement that can be verified by any app on the same phone. Both of these mechanisms are reflected in network RPCs. This allows remote systems visibility into the state of the phone when the RPC was made. We demonstrate the usefulness of Quire with two example applications: an advertising service that runs advertisements separately from their hosting applications, and a remote payment system. We show that Quire's performance overhead is minimal.
Validating a Shortened Depression Scale (10 Item CES-D) among HIV-Positive People in British Columbia, Canada

Objective To establish the reliability and validity of a shortened (10-item) depression scale used among HIV-positive patients enrolled in the Drug Treatment Program in British Columbia, Canada. Methods The 10-item CES-D (Center for Epidemiologic Studies Depression Scale) was examined among 563 participants who initiated antiretroviral therapy (ART) between August 1, 1996 and June 30, 2002. Internal consistency of the scale was measured by Cronbach’s alpha. Using the original CES-D 20 as primary criteria, comparisons were made using the Kappa statistic. Predictive accuracy of CES-D 10 was assessed by calculating sensitivity, specificity, positive predictive values and negative predictive values. Factor analysis was also performed to determine if the CES-D 10 contained the same factors of positive and negative affect found in the original development of the CES-D. Results The correlation between the original and the shortened scale is very high (Spearman correlation coefficient = 0.97 (P<0.001). Internal consistency reliability coefficients of the CES-D 10 were satisfactory (Cronbach α = 0.88). The CES-D 10 showed comparable accuracy to the original CES-D 20 in classifying participants with depressive symptoms (Kappa = 0.82, P<0.001). Sensitivity of CES-D 10 was 91%; specificity was 92%; and positive predictive value was 92%. Factor analysis demonstrates that CES-D 10 contains the same underlying factors of positive and negative affect found in the original development of the CES-D 20. Conclusion The 10-item CES-D is a comparable tool to measure depressive symptoms among HIV-positive research participants.
Ischaemic and haemorrhagic stroke associated with non-vitamin K antagonist oral anticoagulants and warfarin use in patients with atrial fibrillation: a nationwide cohort study

Background Non-vitamin K antagonist (VKA) oral anticoagulants (NOACs) are widely used as stroke prophylaxis in non-valvular atrial fibrillation (AF), but comparative data are sparse. Purpose To compare dabigatran, rivaroxaban, and apixaban vs. VKA and the risk of stroke/thromboembolism (TE) and intracranial bleeding in AF. Methods Using Danish nationwide registries (2011-15), anticoagulant-naïve AF patients were identified when initiating VKA or an NOAC. Outcomes were stroke/TE and intracranial bleeding. Multiple outcome-specific Cox regression was performed to calculate average treatment effects as standardized differences in 1-year absolute risks. Results Overall, 43 299 AF patients initiated VKA (42%), dabigatran (29%), rivaroxaban (13%), and apixaban (16%). Mean CHA2DS2-VASc (SD) score was: VKA 2.9 (1.6), dabigatran 2.7 (1.6), rivaroxaban 3.0 (1.6), and apixaban 3.1 (1.6). Within patient-specific follow-up limited to the first 2 years, 1054 stroke/TE occurred and 261 intracranial bleedings. Standardized absolute risk (95% CI) of stroke/TE at 1 year after initiation of VKA was 2.01% (1.80% to 2.21%). In relation to VKA, the absolute risk differences were for dabigatran 0.11% (-0.16% to 0.42%), rivaroxaban 0.05% (-0.33% to 0.48%), and apixaban 0.45% (-0.001% to 0.93%). For the intracranial bleeding outcome, the standardized absolute risk at 1 year was for VKA 0.60% (0.49% to 0.72%); the corresponding absolute risk differences were for dabigatran -0.34% (-0.47% to - 0.21%), rivaroxaban -0.13% (-0.33% to 0.08%), and apixaban -0.20% (-0.38% to - 0.01%). Conclusions Among anticoagulant-naïve AF patients, treatment with NOACs was not associated with significantly lower risk of stroke/TE compared with VKA, but intracranial bleeding risk was significantly lower with dabigatran and apixaban.
The Experience of Witnessing Patients' Trauma and Suffering Among Acute Care Nurses

A large body of research provides evidence of workplace injuries to those in the nursing profession. Research on workplace stress and burnout among medical professionals is also well known; however, the profession of acute care nursing has not been examined with regards to work-related stress. This qualitative study focused on acute care nurses’ workplace stress, as 5 acute care nurses described experiences related to witnessing patients’ trauma and suffering. Through the use of phenomenological analysis, five main themes emerged from the interviews, revealing a more in-depth understanding of nurses’ experiences in acute care settings. These themes were (a) shock and prolonged witnessing of suffering, (b) long-term effects, (c) distancing as a coping strategy, (d) feelings of guilt and helplessness, and (e) dissonance in core beliefs about self. The results are discussed in terms of coping strategies and recommendations for counsellors working with health care professionals.
Exploiting alignment techniques in MATREX: the DCU machine translation system for IWSLT 2008.

In this paper, we give a description of the machine translati on (MT) system developed at DCU that was used for our third participation in the evaluation campaign of the Internatio nal Workshop on Spoken Language Translation (IWSLT 2008). In this participation, we focus on various techniques for wo rd and phrase alignment to improve system quality. Specifically, we try out our word packing and syntax-enhanced word alignment techniques for the Chinese‐English task and for the English‐Chinese task for the first time. For all translation tasks except Arabic‐English, we exploit li nguistically motivated bilingual phrase pairs extracted fr om parallel treebanks. We smooth our translation tables with out-of-domain word translations for the Arabic‐English and Chinese‐English tasks in order to solve the problem of the high number of out of vocabulary items. We also carried out experiments combining both in-domain and out-of-domain data to improve system performance and, finally, we deploy a majority voting procedure combining a language modelbased method and a translation-based method for case and punctuation restoration. We participated in all the transl ation tasks and translated both the single-best ASR hypotheses and the correct recognition results. The translation results c onfirm that our new word and phrase alignment techniques are often helpful in improving translation quality, and the dat a combination method we proposed can significantly improve system performance.
Outage Analysis of Amplify-and-Forward Partial Relay Selection Scheme with Multiple Interferers

In this letter, the exact form of the outage probability for opportunistic amplify-and-forward (AF) partial relay selection scheme in interference-limited environment is derived. It is assumed that multiple interferers affect only on the relays due to the multicell environment of wireless networks. Analysis in this paper can be an efficient technique for investigating the effect of interference in cooperative AF relaying on the outage probability. We confirm that our analytical results match the simulation results perfectly on all the ranges of signal-to-noise ratio (SNR).
Novel 5′ Untranslated Region Directed Blockers of Iron-Regulatory Protein-1 Dependent Amyloid Precursor Protein Translation: Implications for Down Syndrome and Alzheimer's Disease

We reported that iron influx drives the translational expression of the neuronal amyloid precursor protein (APP), which has a role in iron efflux. This is via a classic release of repressor interaction of APP mRNA with iron-regulatory protein-1 (IRP1) whereas IRP2 controls the mRNAs encoding the L- and H-subunits of the iron storage protein, ferritin. Here, we identified thirteen potent APP translation blockers that acted selectively towards the uniquely configured iron-responsive element (IRE) RNA stem loop in the 5′ untranslated region (UTR) of APP mRNA. These agents were 10-fold less inhibitory of 5′UTR sequences of the related prion protein (PrP) mRNA. Western blotting confirmed that the ‘ninth’ small molecule in the series selectively reduced neural APP production in SH-SY5Y cells at picomolar concentrations without affecting viability or the expression of α-synuclein and ferritin. APP blocker-9 (JTR-009), a benzimidazole, reduced the production of toxic Aβ in SH-SY5Y neuronal cells to a greater extent than other well tolerated APP 5′UTR-directed translation blockers, including posiphen, that were shown to limit amyloid burden in mouse models of Alzheimer's disease (AD). RNA binding assays demonstrated that JTR-009 operated by preventing IRP1 from binding to the IRE in APP mRNA, while maintaining IRP1 interaction with the H-ferritin IRE RNA stem loop. Thus, JTR-009 constitutively repressed translation driven by APP 5′UTR sequences. Calcein staining showed that JTR-009 did not indirectly change iron uptake in neuronal cells suggesting a direct interaction with the APP 5′UTR. These studies provide key data to develop small molecules that selectively reduce neural APP and Aβ production at 10-fold lower concentrations than related previously characterized translation blockers. Our data evidenced a novel therapeutic strategy of potential impact for people with trisomy of the APP gene on chromosome 21, which is a phenotype long associated with Down syndrome (DS) that can also cause familial Alzheimer's disease.
Statistical Prediction Based on Censored Life Data

This article describes methods for using censored life data to construct prediction bounds or intervals for future outcomes. Both new-sample prediction (e.g., using data from a previous sample to make predictions on the future failure time of a new unit) and within-sample prediction problems (e.g., predicting the number of future failures from a sample, based on early data from that sample) are considered. The general method, based on an assumed parametric distribution, uses simulationbased calibration. This method provides exactly the nominal coverage probability when an exact pivotal-based method exists and a highly accurate large-sample approximation, otherwise. To illustrate new-sample prediction, we show how to construct a prediction interval for a single future observation from a previously sampled population/process (motivated by a customer's request for an interval to contain the life of a purchased product). To illustrate within-sample prediction, we show how to compute a prediction interval for .
Biphasic culture strategy based on hyperosmotic pressure for improved humanized antibody production in Chinese hamster ovary cell culture

SummaryHyperosmotic pressure increased specific antibody productivity (qAb) of recombinant Chinese hamster ovary (rCHO) cells (SH2-0.32) and it depressed cell growth. Thus, the use of hyperosmolar medium did not increase the maximum antibody concentration substantially. To overcome this drawback, the feasibility of biphasic culture strategy was investigated. In the biphasic culture, cells were first cultivated in the standard medium with physiological osmolality (294 mOsm/kg) for cell growth. When cells reached the late exponential growth phase, the spent standard medium was replaced with the fresh hyperosmolar medium (522 mOsm/kg) for antibody production. The qAb in growth phase with the standard medium was 2.1 μg per 106 cells/d, whereas the qAb in antibody production phase with the hyperosmolar medium was 11.1 μg per 106 cells/d. Northern blot analysis showed a positive relationship between the relative contents of intracellular immunoglobulin messenger ribonucleic acid and qAb. Because of the enhanced qAb and the increased cell concentration in biphasic culture, the maximum antibody concentration obtained in biphasic culture with 522 mOsm/kg medium exchange was 161% higher than that obtained in batch culture with the standard medium. Taken together, the simple biphasic culture strategy based on hyperosmotic culture is effective in improving antibody production of rCHO cells.
Nonparametric General Reinforcement Learning

Reinforcement learning (RL) problems are often phrased in terms of Markov decision processes (MDPs). In this thesis we go beyond MDPs and consider RL in environments that are non-Markovian, non-ergodic and only partially observable. Our focus is not on practical algorithms, but rather on the fundamental underlying problems: How do we balance exploration and exploitation? How do we explore optimally? When is an agent optimal? We follow the nonparametric realizable paradigm. We establish negative results on Bayesian RL agents, in particular AIXI. We show that unlucky or adversarial choices of the prior cause the agent to misbehave drastically. Therefore Legg-Hutter intelligence and balanced Pareto optimality, which depend crucially on the choice of the prior, are entirely subjective. Moreover, in the class of all computable environments every policy is Pareto optimal. This undermines all existing optimality properties for AIXI. However, there are Bayesian approaches to general RL that satisfy objective optimality guarantees: We prove that Thompson sampling is asymptotically optimal in stochastic environments in the sense that its value converges to the value of the optimal policy. We connect asymptotic optimality to regret given a recoverability assumption on the environment that allows the agent to recover from mistakes. Hence Thompson sampling achieves sublinear regret in these environments. Our results culminate in a formal solution to the grain of truth problem: A Bayesian agent acting in a multi-agent environment learns to predict the other agents' policies if its prior assigns positive probability to them (the prior contains a grain of truth). We construct a large but limit computable class containing a grain of truth and show that agents based on Thompson sampling over this class converge to play Nash equilibria in arbitrary unknown computable multi-agent environments.
Characterizing coal-gasifier slag–refractory interactions

AbstractTo characterize refractory degradation and loss in commercial coal-gasifier combined cycle power systems, cup-type tests were conducted on high chromium-alumina, sinter-bonded refractories under laboratory conditions designed to simulate commercial operations of temperature, atmosphere, and slag interactions. These tests provided qualitative results from which the slag–refractory interactions can be characterized. These high chromium refractories were generally inert with respect to the coal slag components. However, in this study preliminary findings did show (1) iron ( oxide) in the slag reacted with chrome sesquioxide to produce a Cr–Fe spinel at the slag–refractory interface, and (2) chrome was soluble in the molten slag. Comparison of cup-type test results with data from operating commercial plants suggests that the principal loss of refractory material in a coal-gasifier combustion chamber is chrome dissolution into the slag. Tests are currently underway to determine if minor modifications t.