Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Inference by Combining Biologically Motivated Regulatory Constraints with Penalized Regression

Reconstructing biomolecular networks from time series mRNA or protein abundance measurements is a central challenge in computational systems biology. The regulatory processes behind cellular responses are coupled and nonlinear, leading to rich dynamical behavior. One class of reconstruction algorithms uses regression and penalized regression to impose sparseness on the solution, as requested biologically. Motivated by the five‐gene challenge in the Dialogue for Reverse Engineering Assessments and Methods 2 (DREAM2) contest, we extend and test penalized regression schemes both on data from simulations and real qPCR measurements. The methods showing best performance are the Adaptive Ridge (AR) regression and a new extension thereof, in which we impose a biological constraint to the reconstructed network. Specifically, we request from the solutions that the outgoing links have the same regulatory sign, which is a reasonable approximation for most prokaryotic transcriptional networks. In other words, a given regulator must be either an activator or a repressor but not both. The constraints can be implemented with quadratic programming, and we show that this improves the reconstruction performance significantly. While linear models are not sufficiently general to encompass most complex behaviors, they offer powerful tools for network reconstruction, particularly for systems operating near a steady state. In particular, the optimization problems are well behaved and methodologies allow finding global optima efficiently. Adding constraints reflecting biological circuit designs is one of the most important aspects of network inference. We propose one such constraint, namely the consistency in the signs of outgoing links, which will facilitate the inference of transcriptional regulatory networks.
Role of endothelin in microvascular dysfunction following percutaneous coronary intervention for non-ST elevation acute coronary syndromes: a single-centre randomised controlled trial

Objectives Percutaneous coronary intervention (PCI) for acute coronary syndromes frequently fails to restore myocardial perfusion despite establishing epicardial vessel patency. Endothelin-1 (ET-1) is a potent vasoconstrictor, and its expression is increased in atherosclerosis and after PCI. In this study, we aim to define the role of endothelin in regulating coronary microvascular blood flow and myocardial perfusion following PCI in patients with non-ST elevation acute coronary syndromes (NSTACS), by assessing whether adjunctive therapy with a selective endothelin A (ETA) receptor antagonist acutely improves postprocedural coronary microvascular blood flow. Methods In a randomised, double-blinded, placebo-controlled trial, 23 NSTACS patients were enrolled to receive an intracoronary infusion of placebo (n=11) or BQ-123 (n=12) immediately before PCI. Post-PCI coronary microvascular blood flow and myocardial perfusion were assessed by measuring Doppler-derived average peak velocity (APV), and cardiac biomarker levels were quantified. Results Compared with the placebo group, APV was significantly higher in the drug group immediately after PCI (30 (20, 37) vs 19 (9, 26) cm/s; p=0.03). Hyperaemic APV, measured post-adenosine administration, was higher in the BQ-123 group, but the difference did not achieve statistical significance (56 (48, 72) vs 46 (34, 64) cm/s; p=0.090). Maximum coronary flow reserve postprocedure was not different between the two groups (2.1 (1.6, 2.3) vs 2.5 (1.8, 3.0)). Per cent change in creatine kinase isoenzyme MB from the time of PCI to 8 and 16 hours post-PCI was significantly lower in the drug group compared with the placebo group (−17 (−26, −10) vs 26 (−15, 134); p=0.02 and −17 (−38, 14) vs 107 (2, 446); p=0.007, respectively). Conclusions Endothelin is a mediator of microvascular dysfunction during PCI in NSTACS, and adjunctive selective ETA antagonist may augment myocardial perfusion during PCI. Trial registration number NCT00586820; Results.
The Utility and Applicability of Chronic Myeloid Leukemia Scoring Systems for Predicting the Prognosis of Egyptian Patients on Imatinib: Retrospective Study

Background: Chronic myeloid leukemia (CML) is myeloproliferative clonal neoplasm. Imatinib has greatly improved CML prognosis. Many prognostic scoring systems have been developed for CML risk stratification. In clinical practice, 3 systems are widely used: Sokal, Hasford and European Treatment Outcome Study (EUTOS). Recently, EUTOS long-term survival (ELTS) score is the first long-term scoring system that considered specifically CML-related death. Therefore, the aim of the present study was to validate the effectiveness of Sokal, Hasford, EUTOS and ELTS scoring systems in predicting the outcome in Egyptian CML-chronic phase (CML-CP) patients treated with imatinib. Patients and methods: Retrospective study performed on 167 patients with CML-CP who were treated with imatinib. Using the Sokal, Hasford, EUTOS and ELTS scores, we divided the patients into each risk groups. Results: Significant differences in event free survival (EFS), time without progression (TWP) and overall survival (OS) prediction between the Sokal, Hasford and ELTS risk groups, but no significant difference among the EUTOS score risk groups. Conclusion: Our study indicates that Sokal, Hasford and ELTS scoring systems but not the EUTOS score are effective in predicting early treatment response, EFS, TWP and OS for Egyptian CML patients treated with imatinib
Evaluation of different strategies for domain adaptation in opinion mining

The work presented in this article takes place in the field of opinion mining and aims more particularly at finding the polarity of a text by relying on machine learning methods. In this context, it focuses on studying various strategies for adapting a statistical classifier to a new domain when training data only exist for one or several other domains. This study shows more precisely that a self-training procedure consisting in enlarging the initial training corpus with texts from the target domain that were reliably classified by the classifier is the most successful and stable strategy for the tested domains. Moreover, this strategy gets better results in most cases than (Blitzer et al., 2007)’s method on the same evaluation corpus while it is more simple.
The BCMA gene, preferentially expressed during B lymphoid maturation, is bidirectionally transcribed.

In a previous study of a t(4;16)(q26;p13) translocation, found in a human malignant T-cell lymphoma the BCMA gene, located on chromosome band 16p13.1, has been characterized. In this study we show that the BCMA gene is organized into three exons and its major initiation transcription site is located 69 nucleotides downstream of a TATA box. RNase protection assays demonstrated that the BCMA gene is preferentially expressed in mature B cells, suggesting a role for this gene in the B-cell developmental process. A cDNA complementary to the BCMA cDNA was cloned and sequenced and its presence was assessed by RNase protection assay and anchor-PCR amplification. This antisense-BCMA RNA is transcribed from the same locus as BCMA, and exhibits mRNA characteristic features, e.g. polyadenylation and splicing. It also contains an ORF encoding a putative 115 aa polypeptide, presenting no homology with already known sequences. RNase protection assays demonstrated the simultaneous expression of natural sense and antisense-BCMA transcripts in the majority of human B-cell lines tested.
Salivary Immunoglobulin A Secretion Rate Is Negatively Associated with Cancer Mortality: The West of Scotland Twenty-07 Study

Immunoglobulins are essential for combating infectious disease although very high levels can indicate underlying pathology. The present study examined associations between secretory immunoglobulin A (sIgA) in saliva and mortality rates in the general population. Participants were 639 adults from the eldest cohort of the West of Scotland Twenty-07 Study aged 63 years at the time of saliva sampling in 1995. From unstimulated 2-minute saliva samples, saliva volume and S-IgA concentration were measured, and S-IgA secretion rate determined as their product. Mortality data were tracked for 19 years. Cox proportional hazard models were applied to compute hazard ratios (HR) for all-cause mortality from sIgA secretion rate. Associations were adjusted for gender, assay batch, household occupational group, smoking, medication usage, and self-reported health. There was a negative association between log sIgA secretion rate and all-cause mortality, HR = 0.81, 95%CI = 0.73–0.91, p < . 001. Further analysis of specific causes of mortality revealed that the all-cause association was due to an underlying association with cancer mortality and in particular with cancers other than lung cancer. The HR for non-lung cancer was 0.68 (95%CI = 0.54 to 0.85) implying a 32% reduction in mortality risk per standard deviation rise in log sIgA secretion rate. Effects were stronger for men than women. For deaths from respiratory diseases, sIgA secretion had a non-linear relationship with mortality risk whereby only the very lowest levels of secretion were associated with elevated risk. SIgA concentration revealed a similar but weaker pattern of association. In the present study, higher secretion rates of sIgA were associated with a decreased risk of death from cancer, specifically non-lung cancer, as well as from respiratory disease. Thus, it appears that sIgA plays a protective role among older adults, and could serve as a marker of mortality risk, specifically cancer mortality.
CXCL12 overexpression and secretion by aging fibroblasts enhance human prostate epithelial proliferation in vitro

The direct relationship between the aging process and the incidence and prevalence of both benign prostatic hyperplasia (BPH) and prostate cancer (PCa) implies that certain risk factors associated with the development of both diseases increase with the aging process. In particular, both diseases share an overly proliferative phenotype, suggesting that mechanisms that normally act to suppress cellular proliferation are disrupted or rendered dysfunctional as a consequence of the aging process. We propose that one such mechanism involves changes in the prostate microenvironment, which ‘evolves’ during the aging process and disrupts paracrine interactions between epithelial and associated stromal fibroblasts. We show that stromal fibroblasts isolated from the prostates of men 63–81 years of age at the time of surgery express and secrete higher levels of the CXCL12 chemokine compared with those isolated from younger men, and stimulate CXCR4‐mediated signaling pathways that induce cellular proliferation. These studies represent an important first step towards a mechanistic elucidation of the role of aging in the etiology of benign and malignant prostatic diseases.
Systematic Co-Evolution of OCL Expressions

Metamodels are the central artifacts in Model-Driven Engineering and like any other software artifact, subject to constant change. This fact necessitates the co-evolution of dependent artifacts such as models and transformations to resolve induced inconsistencies. While the co-evolution of models has been extensively studied, the co-evolution of transformations and especially OCL expressions being a substantial part thereof have been less examined so far. To fill this gap, this paper proposes resolution actions for all atomic metamodel changes violating the syntactic correctness of OCL expressions, thus, being able to resolve induced inconsistencies. Thereby, the resolution actions establish an emulated view on the evolved metamodel such that syntactic correctness is re-established. To verify the semantic correctness of the resolution actions, we use our PaMoMo language, allowing us to specify semantic correctness requirements for model transformations. Finally, to demonstrate the applicability of our approach, a proofof-concept prototype based on ATL is provided.
Comparative Analysis of Vocabulary Learning Strategies in Learning English as a Foreign Language among Freshmen and Senior Medical Sciences Students Across Different Fields of Study

Learning strategies play an important role in the development of language skills. Vocabulary learning strategies, regarded as the backbone of these strategies, have become a major part of English language teaching. This study aims to compare use and preference of Vocabulary Learning Strategies (VLS) among freshmen and senior EFL medical sciences students across different fields of study. 449 students participated in the study, of which 64.6% were female and 35.4% were male. The instrument utilized in this research was a questionnaire consisting of 41 items related to the students’ approach to vocabulary learning. The items were classified under eight sections as dictionary strategies, guessing strategies, study preferences, memory strategies, autonomy, note- taking strategies, selective attention, and social strategies. The results indicated that freshmen students, particularly students majoring in surgical technology used memorisation technique followed by dictionary use and note taking strategies more than the senior students. In particular, male students were more autonomous while female students preferred to use social strategies. Overall, guessing and dictionary strategies were the most frequently used strategies among all the learners (p=0.000). Based on the results, which indicated more strategy use by the freshmen students, it is recommended that language teachers recognize the different needs of the students at different levels, and adjust teaching and learning procedures accordingly.
"Reasonable Accommodation" and "Accessibility": Human Rights Instruments Relating to Inclusion and Exclusion in the Labor Market

Ableism is a powerful social force that causes persons with disabilities to suffer exclusion. The UN Convention on the Rights of Persons with Disabilities (CRPD) is based on the human rights principles of equality and freedom for all people. This Convention contains two human rights instruments: the principle of accessibility and the means of reasonable accommodation, which can be used to protect the human rights of disabled persons. The extent to which they are used depends on whether the state implements the Convention adequately and whether companies accept their responsibility with respect to employing disabled persons and making workplaces available and designing them appropriately. Civil society can demand the adequate implementation of the human rights asserted in the CRPD and, thus, in national legislation, as well. A crucial point here is that only a state that has ratified the Convention is obliged to implement the Convention. Civil society has no obligation to do this, but has the right to participate in the implementation process (Art. 4 and Art. 33 CRPD). The Convention can play its part for disabled persons participating in the labor market without discrimination. If it is not implemented or not heeded sufficiently, the state must push this and put more effort into its implementation. If the state does not do this, this violates human rights and has direct consequences for the living conditions of disabled persons. The powerful ideological force of ableism then remains dominant and hampers or prevents the participation of persons with disabilities in the labor market and, thus, in society as a whole.
The presence of a culturally similar or dissimilar social partner affects neural responses to emotional stimuli

Background Emotional responding is sensitive to social context; however, little emphasis has been placed on the mechanisms by which social context effects changes in emotional responding. Objective We aimed to investigate the effects of social context on neural responses to emotional stimuli to inform on the mechanisms underpinning context-linked changes in emotional responding. Design We measured event-related potential (ERP) components known to index specific emotion processes and self-reports of explicit emotion regulation strategies and emotional arousal. Female Chinese university students observed positive, negative, and neutral photographs, whilst alone or accompanied by a culturally similar (Chinese) or dissimilar researcher (British). Results There was a reduction in the positive versus neutral differential N1 amplitude (indexing attentional capture by positive stimuli) in the dissimilar relative to alone context. In this context, there was also a corresponding increase in amplitude of a frontal late positive potential (LPP) component (indexing engagement of cognitive control resources). In the similar relative to alone context, these effects on differential N1 and frontal LPP amplitudes were less pronounced, but there was an additional decrease in the amplitude of a parietal LPP component (indexing motivational relevance) in response to positive stimuli. In response to negative stimuli, the differential N1 component was increased in the similar relative to dissimilar and alone (trend) context. Conclusion These data suggest that neural processes engaged in response to emotional stimuli are modulated by social context. Possible mechanisms for the social-context-linked changes in attentional capture by emotional stimuli include a context-directed modulation of the focus of attention, or an altered interpretation of the emotional stimuli based on additional information proportioned by the context.
Information Acquisition and Reputation Dynamics

We study reputation games where a long-lived player with a possible commitment faces a sequence of short-lived players who must pay to observe the long-lived player's past behavior. In this costly information model we show that equilibrium behavior is cyclical. The long-lived player builds her reputation up only to exploit it; then builds it up again, and so on. We call this behavior reputation renewal and show that for a wide class of reputation games as well as for a host of possible alternatives to the information cost structure, all equilibria display reputation renewal. We provide a method to construct the equilibria, and explicitly construct an essentially unique equilibrium for the case of linear cost functions. We also find that in the reputation renewal equilibria, the short-lived players always randomize how much information they purchase, but play pure strategies once the information is obtained.
TAS2R38 and Its Influence on Smoking Behavior and Glucose Homeostasis in the German Sorbs

Background Genetic variants within the bitter taste receptor gene TAS2R38 are associated with sensitivity to bitter taste and are related to eating behavior in the Amish population. Sensitivity to bitter taste is further related to anthropometric traits in an genetically isolated Italian population. We tested whether the TAS2R38 variants (rs713598; rs1726866 and rs10246939) may be related to eating behavior, anthropometric parameters, metabolic traits and consumer goods intake in the German Sorbs. Materials and Methods The three SNPs were genotyped in a total cohort of 1007 individuals (male/female: 405/602). The German version of the three-factor eating questionnaire was completed by 548 individuals. Genetic association analyses for smoking behavior, alcohol and coffee intake, eating behavior factors (restraint, disinhibition and hunger) and other metabolic traits were analyzed. Further, by combining the three SNPs we applied comparative haplotype analyses categorizing PAV (proline-alanine-valine) carriers (tasters) vs. homozygous AVI (alanin-valine-isoleucine) carriers (non-tasters). Results Significant associations of genetic variants within TAS2R38 were identified with percentage of body fat, which were driven by associations in women. In men, we observed significant associations with 30 min plasma glucose, and area under the curve for plasma glucose (0–120 min) (all adjusted P≤0.05). Further, we found that carriers of at least one PAV allele show significantly lower cigarette smoking per day (P = 0.002) as well as, albeit non-significant, lower alcohol intake. We did not confirm previously reported associations between genetic variants of TAS2R38 and eating behavior. Conclusion Our data suggest that genetic variation in TAS2R38 is related to individual body composition measures and may further influence consumer goods intake in the Sorbs possibly via individual sensitivity to bitter taste.
Traditional Formula, Modern Application: Chinese Medicine Formula Sini Tang Improves Early Ventricular Remodeling and Cardiac Function after Myocardial Infarction in Rats

Sini Tang (SNT) is a traditional Chinese herbal formula consisting of four different herbs: the root of Aconitum carmichaelii, the bark of Cinnamomum cassia, the rhizome of Zingiber officinale, and the root of Glycyrrhiza uralensis. This study aims to evaluate the improvement of early ventricular remodeling and cardiac function in myocardial infarction (MI) rats by SNT. A MI model was established by ligation of the left anterior descending coronary artery. Following treatment for 4 weeks, ultrasonic echocardiography was performed. Myocardial histopathological changes were observed using haematoxylin and eosin staining. Collagens (type I and type III), transforming growth factor-β1 (TGF-β1), and Toll-like receptors (TLR-2 and TLR-4) were measured in plasma, serum, and myocardial tissue. SNT treatment decreased the infarct size, the left ventricular cavity area/heart cavity area ratio, and the left ventricle dimension at end systole and increased the left ventricular ejection fraction. SNT reduced the levels of TLR-2 and TLR-4 in myocardial tissue significantly and decreased the collagens content in serum and in myocardial tissue. SNT could partially reduce the level of TGF-β1 in serum and in myocardial tissue. Our data suggest that the Chinese medicine formula SNT has the potential to improve early ventricular remodeling and cardiac function after MI.
Understanding the Structure of Autonomy among Filipino Adolescents

This study examined the structure of autonomy among Filipino adolescents through the framework proposed by Markus and Kitayama (1991b). Screening through median split was used to identify participants with high level of interdependence. The first set of participants (n=21) responded in the qualitative phase while the second set of participants (n=201) participated in the quantitative phase. After performing exploratory factor analysis (EFA), two dimensions of autonomy emerged—inward autonomy and outward autonomy. The results provide evidence about the unique definition of autonomy in an interdependent culture like the Philippines. Implications to assessment and student motivation are discussed.