Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in cognitive distortions and affectivity levels in adolescent depression after acute phase fluoxetine treatment

ABSTRACT Introduction: It is supposed that both antidepressants and psychotherapies work in a manner consistent with cognitive theories of depression when changing negative affective and cognitive distortions. This study evaluated changes in cognitive distortions (i.e. systematic misinterpretations of new information) and affectivity in adolescent major depressive disorder (MDD) after acute phase treatment with fluoxetine. Methods: Twenty-five adolescents (mean age 15.10 years (SD = 1.19); 17 (68%) females) with MDD receiving fluoxetine were followed for 8 weeks. Clinician rating scales of MDD and self-reports of cognitive distortions and affectivity were completed before and after the treatment. Results: Seven (28%) adolescents showed significant improvement in cognitive distortions, 11 (44%) showed a significant decrease in negative affect, and 15 (60%) showed a significant increase in positive affect. The responders to fluoxetine had significantly decreased level of negative affect (62.5%) and an increased level in positive affect (81.2%) compared to non-responders, whereas there were no differences between the two regarding changes in cognitive distortions. Conclusions: Treatment with fluoxetine over 8 weeks led to reductions in cognitive distortions, with decreased negative and increased positive affect in adolescents with MDD. Improvements in affectivity levels closely corresponded to reductions in depressive symptoms and were greater than improvements in cognitive distortions.
CFSH: Factorizing sequential and historical purchase data for basket recommendation

To predict what products customers will buy in next transaction is an important task. Existing work in next-basket prediction can be summarized into two paradigms. One is the item-centric paradigm, where sequential patterns are mined from customers’ transactional data and leveraged for prediction. However, these approaches usually suffer from the data sparseness problem. The other is the user-centric paradigm, where collaborative filtering techniques have been applied on customers’ historical data. However, these methods ignore the sequential behaviors of customers which is often crucial for next-basket prediction. In this paper, we introduce a hybrid method, namely the Co-Factorization model over Sequential and Historical purchase data (CFSH for short) for next-basket recommendation. Compared with existing methods, our approach conveys the following merits: 1) By mining global sequential patterns, we can avoid the sparseness problem in traditional item-centric methods; 2) By factorizing product-product and customer-product matrices simultaneously, we can fully exploit both sequential and historical behaviors to learn customer and product representations better; 3) By using a hybrid recommendation method, we can achieve better performance in next-basket prediction. Experimental results on three real-world purchase datasets demonstrated the effectiveness of our approach as compared with the state-of-the-art methods.
Physicians’ views on patient participation in choice of oral anticoagulants in atrial fibrillation—a qualitative study

Direct oral anticoagulants provide an alternative to vitamin K antagonists for the anticoagulation therapy in atrial fibrillation (AF). The availability of several treatment options with different attributes makes shared decision‐making appropriate for the choice of anticoagulation therapy. The aim of this study was to understand how physicians choose an oral anticoagulant (OAC) for patients with AF and how physicians view patients’ participation in this decision. Semi‐structured interviews with 17 Finnish physicians (eight general practitioners and nine specialists) working in the public sector were conducted. An interview guide on experience, prescribing and opinions about oral anticoagulants was developed based on previous literature. The data were thematically analysed using deductive and inductive approaches. Based on the interviews, patient's opinion was the most influential factor in decision‐making when there were no clinical factors limiting the choice between OACs. Of patient's preferences, the most important was the attitude towards co‐payments of OACs. Patients’ opinions on monitoring of treatment, dosing and antidote availability were also mentioned by the interviewees. The choice of an OAC in AF was patient‐centred as all interviewees expressed that patient's opinion affects the choice.
Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters.

BACKGROUND The human monoamine transporters (hMATs) primary including hSERT, hNET and hDAT are important targets for the treatment of depression and other behavioral disorders with more than availability of 30 approved drugs. OBJECTIVE This paper is to review the recent progress in the binding mode and inhibitory mechanism of hMATs inhibitors with the central or allosteric binding sites, for the benefit of future hMATs inhibitor design and discovery. The structure-activity relationship (SAR) and the selectivity for hit/lead compounds to hMATs that evaluated by in vitro and in vivo experiments will be highlighted. METHODS PubMed and Web of Science database were searched for protein-ligand interaction, novel inhibitors design and synthesis studies related to hMATs. RESULTS Literature data indicate that since the first crystal structure determinations of the homologous bacterial leucine transporter (LeuT) complexed with clomipramine, a sizable database of over 100 experimental structures or computational models has been accumulated that now defines a substantial degree of structural variability hMATs-ligands recognition. In the meanwhile, a number of novel hMATs inhibitors have been discovered by medicinal chemistry with significant help from computational models. CONCLUSION The reported new compounds act on hMATs as well as the structures of the transporters complexed with diverse ligands by either experiment or computational modeling have shed light on the poly-pharmacology, multimodal and allosteric regulation of the drugs to transporters. All of the studies will greatly promote the structure-based drug design (SBDD) of structurally novel scaffolds with high activity and selectivity for hMATs.
Cytoplasmic p21 Mediates 5-Fluorouracil Resistance by Inhibiting Pro-Apoptotic Chk2

The oncogenic cytoplasmic p21 contributes to cancer aggressiveness and chemotherapeutic failure. However, the molecular mechanisms remain obscure. Here, we show for the first time that cytoplasmic p21 mediates 5-Fluorouracil (5FU) resistance by shuttling p-Chk2 out of the nucleus to protect the tumor cells from its pro-apoptotic functions. We observed that cytoplasmic p21 levels were up-regulated in 5FU-resistant colorectal cancer cells in vitro and the in vivo Chorioallantoic membrane (CAM) model. Kinase array analysis revealed that p-Chk2 is a key target of cytoplasmic p21. Importantly, cytoplasmic form of p21 mediated by p21T145D transfection diminished p-Chk2-mediated activation of E2F1 and apoptosis induction. Co-immunoprecipitation, immunofluorescence, and proximity ligation assay showed that p21 forms a complex with p-Chk2 under 5FU exposure. Using in silico computer modeling, we suggest that the p21/p-Chk2 interaction hindered the nuclear localization signal of p-Chk2, and therefore, the complex is exported out of the nucleus. These findings unravel a novel mechanism regarding an oncogenic role of p21 in regulation of resistance to 5FU-based chemotherapy. We suggest a possible value of cytoplasmic p21 as a prognosis marker and a therapeutic target in colorectal cancer patients.
The Role of Artefacts in Creating a Common Operational Picture During Large Crises

This paper is about the work that takes place during large police operations in different command post settings, and how artefacts are used in the collaborative process in creating a common operational picture (COP). We apply "artefactual multiplicity" as our analytical lens. An interpretative research approach has been applied in form of ethnographical field studies using observation and informal interviews as data collection techniques. The artefacts that have been studied are definable as common artefacts, i.e. artefacts that are commonly available in our work environment. Based upon the five separate studies, the artefacts studied are found to be very important as collaborative tools and many also have embedded visualization functionalities. The main contribution from this research is 1) extensive knowledge about how the artefacts are used in the establishment of the COP during large police operations, where the process of establishing the COP is, to a very large extent, dependent upon the artefacts' collaborative and multiple functions; 2) the proposal and suggestion to study the whole staff and the artefacts used by the staff as one heterogeneous unit, as a record of activities. Studies of single artefacts in isolation reduce the possibility of seeing the full multiplicity of all the artefacts used within the staff, and the complexity of the intertwined web of artefactual functions.
Non-linear process convolutions for multi-output Gaussian processes

The paper introduces a non-linear version of the process convolution formalism for building covariance functions for multi-output Gaussian processes. The non-linearity is introduced via Volterra series, one series per each output. We provide closed-form expressions for the mean function and the covariance function of the approximated Gaussian process at the output of the Volterra series. The mean function and covariance function for the joint Gaussian process are derived using formulae for the product moments of Gaussian variables. We compare the performance of the non-linear model against the classical process convolution approach in one synthetic dataset and two real datasets.
Prepubertal skeletal muscle growth requires Pax7-expressing satellite cell-derived myonuclear contribution

ABSTRACT The functional role of Pax7-expressing satellite cells (SCs) in postnatal skeletal muscle development beyond weaning remains obscure. Therefore, the relevance of SCs during prepubertal growth, a period after weaning but prior to the onset of puberty, has not been examined. Here, we have characterized mouse skeletal muscle growth during prepuberty and found significant increases in myofiber cross-sectional area that correlated with SC-derived myonuclear number. Remarkably, genome-wide RNA-sequencing analysis established that post-weaning juvenile and early adolescent skeletal muscle have markedly different gene expression signatures. These distinctions are consistent with extensive skeletal muscle maturation during this essential, albeit brief, developmental phase. Indelible labeling of SCs with Pax7CreERT2/+; Rosa26nTnG/+ mice demonstrated SC-derived myonuclear contribution during prepuberty, with a substantial reduction at puberty onset. Prepubertal depletion of SCs in Pax7CreERT2/+; Rosa26DTA/+ mice reduced myofiber size and myonuclear number, and caused force generation deficits to a similar extent in both fast and slow-contracting muscles. Collectively, these data demonstrate SC-derived myonuclear accretion as a cellular mechanism that contributes to prepubertal hypertrophic skeletal muscle growth. Summary: Examination of gene expression and morphological changes in mouse skeletal muscle during prepuberty demonstrates that satellite cell-derived myonuclear accretion contributes to prepubertal hypertrophic skeletal muscle growth.
Prognostic significance of midline shift of the olfactory or frontal lobes of the brain in canine nasal carcinomas treated by palliative radiotherapy: a pilot study

Canine nasal carcinomas are often treated with radiotherapy. Presence of lysis of the cribriform plate by tumor invasion (stage 4 by modified Adams’s staging system) is a well-known prognostic factor. In this study, dogs with stage 4 disease were divided into two subgroups based on the presence or absence of midline shift of the olfactory or frontal lobes of the brain (Stage 4a: without presence of midline shift. Stage 4b: with midline shift). The median survival time of dogs with midline shift was significantly shorter than that of dogs without midline shift (64 vs. 208 days). Our results indicate that the finding of a midline shift might have a prognostic significance in dogs with nasal carcinoma treated with radiotherapy.
Characterization of gene expression changes over healthy term pregnancies

During pregnancy, women experience numerous physiological changes but, to date, there is limited published data that characterize accompanying changes in gene expression over pregnancy. This study sought to characterize the complexity of gene expression over the course of pregnancy among women with healthy pregnancies. Subjects provided a venous blood sample during early (6-15 weeks) and late (22-33 weeks) pregnancy, which was used to isolate peripheral blood mononuclear cells prior to RNA extraction. Gene expression was examined for 63 women with uncomplicated, term deliveries. We evaluated the association between weeks gestation at sample collection and expression of each transcript. Of the 16,311 transcripts evaluated, 439 changed over pregnancy after a Bonferroni correction to account for multiple comparisons. Genes whose expression changed over pregnancy were associated with oxygen transport, the immune system, and host response to bacteria. Characterization of changes in gene expression over the course of healthy term pregnancies may enable the identification of genes whose expression predicts complications or adverse outcomes of pregnancy.
Nursing consultation software for hypertensive users of the Family Health Strategy.

OBJECTIVE To report the development of a nursing consultation software for hypertensive users of the Family Health Strategy. METHOD Applied methodological research based on Roger Pressman's Software Engineering, developed in three cycles: planning, composed of the definition of the database prototyping and modelling; development of the navigation interface; and development of functional expressions and programming. RESULT The software consists of administrative and nursing consultation screens. In the history, there is the option of undertaking the first and next consultation; nursing diagnoses are suggested by the system after entering information and can be selected by nurses. Interventions for diagnoses are suggested and can be chosen by nurses after structuring the medical plan. CONCLUSION It is believed that the introduction of computer technology for nursing consultation brings several contributions, such as standardization, integration with different information systems, and continuous update.
Pharmacokinetics, Pharmacodynamics, and Modulation of Hepatic Glucose Production With Insulin Glargine U300 and Glargine U100 at Steady State With Individualized Clinical Doses in Type 1 Diabetes

OBJECTIVE This study characterized the pharmacokinetics (PK), pharmacodynamics (PD), and endogenous (hepatic) glucose production (EGP) of clinical doses of glargine U300 (Gla-300) and glargine U100 (Gla-100) under steady-state (SS) conditions in type 1 diabetes mellitus (T1DM). RESEARCH DESIGN AND METHODS T1DM subjects (N = 18, age 40 ± 12 years, T1DM duration 26 ± 12 years, BMI 23.4 ± 2 kg/m2, A1C 7.19 ± 0.52% [55 ± 5.7 mmol · mol−1−1]) were studied after 3 months of Gla-300 or Gla-100 (evening dosing) titrated to fasting euglycemia (random, crossover) with the euglycemic clamp using individualized doses (Gla-300 0.35 ± 0.08, Gla-100 0.28 ± 0.07 units · kg−1). RESULTS Plasma free insulin concentrations (free immunoreactive insulin area under the curve) were equivalent over 24 h with Gla-300 versus Gla-100 (point estimate 1.11 [90% CI 1.03; 1.20]) but were reduced in the first 6 h (0.91 [90% CI 0.86; 0.97]) and higher in the last 12 h postdosing (1.38 [90% CI 1.21; 1.56]). Gla-300 and Gla-100 both maintained 24 h euglycemia (0.99 [90% CI 0.98; 1.0]). The glucose infusion rate was equivalent over 24 h (1.03 [90% CI 0.88; 1.21]) but was lower in first (0.77 [90% CI 0.62; 0.95]) and higher (1.53 [90% CI 1.23; 1.92]) in the second 12 h with Gla-300 versus Gla-100. EGP was less suppressed during 0–6 h but more during 18–24 h with Gla-300. PK and PD within-day variability (fluctuation) was 50% and 17% lower with Gla-300. CONCLUSIONS Individualized, clinical doses of Gla-300 and Gla-100 resulted in a similar euglycemic potential under SS conditions. However, Gla-300 exhibited a more stable profile, with lower variability and more physiological modulation of EGP compared with Gla-100.
Evaluation of the Seegene Allplex™ Respiratory Panel for diagnosis of acute respiratory tract infections

ABSTRACT Objectives: The Seegene AllplexTM Respiratory panel was retrospectively challenged using a collection of quality control samples (QCMD) and clinical samples previously analysed with validated routine methods. Methods: A collection of 111 samples [43 QCMD samples, 13 bronchoalveolar lavage fluids and 55 nasopharyngeal aspirates/swabs] was tested with Seegene AllplexTM. The clinical samples were tested previously using either FTD® Respiratory Pathogens 21 qPCR assay (Fast Track Diagnostics), an in-house multiplex PCR for Bordetella, or BioGX Sample-ReadyTM Atypical pneumo panel (Becton Dickinson). Samples were stored at −80°C prior to analysis with Seegene Allplex™, nucleic acids were automatically extracted with NucliSENS Easymag (bioMérieux). Samples returning discordant results were subjected to repeat testing and/or additional testing by reference laboratories. Results: Seegene correctly identified 41/43 QCMD samples (95.4%); two samples positive for respiratory syncytial virus (RSV) and human metapneumovirus, respectively, were only correctly identified following repeat testing. In the 56 clinical samples, overall, 97 pathogens were identified: 65 pathogens (67.0%) were detected both by routine methods and Seegene, 24 pathogens (24.7%) only by routine methods, and 8 pathogens (8.2%) only by Seegene. The majority of discordant results was detected in samples with low pathogen load (22/32, 68.8%) and in samples containing multiple pathogens (25/32, 78.1%). Full agreement between methods was observed for influenza, RSV, adenovirus, Bordetella (para)pertussis and Chlamydia pneumoniae. Discordance was observed for human metapneumovirus, coronavirus OC43, bocavirus and parainfluenza virus, mainly type 4. Conclusion: Overall, the Seegene AllplexTM assay performed well for routine detection of important respiratory targets. Acceptable agreement was observed between Seegene and other routine assays.
Theoretical analysis of balanced truncation for linear switched systems

Abstract In this paper we present a theoretical analysis of the model reduction algorithm for linear switched systems from Shaker and Wisniewski (2011, 2009). This algorithm is based on balanced truncation. More precisely, ( 1 ) we provide a bound on the approximation error in L 2 norm, ( 2 ) we provide a system theoretic interpretation of grammians and their singular values, ( 3 ) we show that the performance of balanced truncation depends only on the input-output map and not on the choice of the state-space representation. In addition, we also show that quadratic stability and LMI estimates of the L 2 gain also depend only on the input-output map.
Gradient-based algorithm for designing sensing matrix considering real mutual coherence for compressed sensing systems

This study deals with the issue of designing the sensing matrix for a compressed sensing (CS) system assuming that the dictionary is given. Traditionally, the measurement of small mutual coherence is considered to design the optimal sensing matrix so that the Gram of the equivalent dictionary is as close to the target Gram as possible, where the equivalent dictionary is not normalised. In other words, these algorithms are designed to solve the CS problem using an optimisation stage followed by normalisation. To achieve a global solution, a novel strategy of the sensing matrix design is proposed by using a gradient-based method, in which the measure of real mutual coherence for the equivalent dictionary is considered. According to this approach, a minimised objective function based on alternating minimisation is also developed through searching the target Gram within a set of relaxed equiangular tight frames. Some experiments are done to compare the performance of the newly designed sensing matrix with the existing ones under the condition that the dictionary is fixed. For the simulations of synthetic data and real image, the proposed approach provides better signal reconstruction accuracy.
Go with the Flow: Graphs, Streaming and Relational Computations over Distributed Dataflow

Author(s): Xin, Reynold Shi | Advisor(s): Franklin, Michael; Stoica, Ion | Abstract: Modern data analysis is undergoing a ``Big Data'' transformation: organizations are generating and gathering more data than ever before, in a variety of formats covering both structured and unstructured data, and employing increasingly sophisticated techniques such as machine learning and graph computation beyond the traditional roll-up and drill-down capabilities provided by SQL. To cope with the big data challenges, we believe that data processing systems will need to provide fine-grained fault recovery across a larger cluster of machines, support both SQL and complex analytics efficiently, and enable real-time computation.This dissertation builds on Apache Spark, a distributed dataflow engine, and creates three related systems: Spark SQL, Structured Streaming, and GraphX. Spark SQL combines relational and procedural processing through a new API called DataFrame. It also includes an extensible query optimizer to support a wide variety of data sources and analytic workloads. Structured Streaming extends Spark SQL's DataFrame API and query optimizer to automatically incrementalize queries, so users can reason about real-time stream data as batch datasets, and have the same application operate over both stream data and batch data. GraphX recasts graph specific system optimizations as dataflow optimizations, and provides an efficient framework for graph computation on top of Spark.The three systems have enjoyed wide adoption in industry and academia, and together they laid the foundation for Spark's 2.0 release. They demonstrate the feasibility and advantages of unifying disparate, specialized data systems on top of distributed dataflow systems.
IT infrastructure at the Rio de Janeiro City Operations Center - the case of 2016 Olympic and Paralympic Games

Rio Operations Center (COR) was the agency of Rio de Janeiro Prefecture responsible for monitoring the Rio 2016 Olympic and Paralympic Games operations, due to its role in the integrated management of the city operations. This paper presents a case study considering a brief theoretical reference and data collected through direct observations, interviews, internal documents and access to the systems and software used by COR. The analysis of the COR IT infrastructure and monitoring teams’ preparation for the Olympics revealed a successful development of new teams and conflict solving practice. Despite the use of different sources of information and the development of specific systems for the event, the COR preparation faced some restrictions in analytical functions, security and integration among systems. Nevertheless, regionalization for monitoring and interagency coordination, cross-agency instant messaging, and a team for active monitoring of social media emerged as new practices, representing opening venues for future research.