Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Archival Texts to Create Network Graphs of Musicians in Early Modern Venice

This project uses network graphs to depict musicians’ careers in late seventeenth-century Venice. The current network graph, viewable on the Musicians in Venice web page, demonstrates relationships between musicians and the institutions that employed them. The graph is bimodal, with nodes representing musicians (“people” nodes) and institutions (“place” nodes). Archival texts are incorporated into the visualization, with transcriptions of records that indicate musicians’ activity included in the node attributes. The entire project is text-based, with data derived from XML transcriptions of archival records in addition to assigned metadata. The current website is a proof of concept for a larger project that would demonstrate ways of displaying text as part of the network graph and using texts in creating network visualizations. The current graph focuses on the career of the composer Giovanni Legrenzi. Legrenzi worked for several prominent Venetian institutions from the early 1670s to his death in 1690 and ultimately was appointed to the most prestigious musical posts in the city. The musicians he worked with also served multiple institutions, either simultaneously or in succession, and their relationships with other musicians, patrons, and administrators often facilitated their movement between institutions. Legrenzi’s Venetian career presents an excellent case study of these musical connections in late seventeenth-century Venice, and studying these connections demonstrates how networks of musicians functioned in this time period. This study also provides a representative sample of how network visualization effectively demonstrates patterns in musicians’ careers in Venice. The texts in the network graph include transcribed administrative documents, mostly unpublished, from the Venetian institutions where Legrenzi was active between 1670 and 1690. These are primarily payment, hiring, and termination records, which document the activity of the musicians employed by or affiliated with these institutions. Several generations of musicologists have used these documents to identify where different musicians were working, when they were employed, and in what capacity (Bonta, 1964; Moore, 1981; Termini, 1981; and Selfridge-Field, 1994). In this sense, this treatment of the documents is standard to the field, but applies DH methodology and processes to create visual representations the data. This provides a new perspective on the sources. For instance, grouping the “person” nodes by centrality results in multiple sub-groups, and proximity among these nodes demonstrates shared institutions and implied communities. (Hanneman and Riddle, 2005: Chapter 10) (Mary Russell Mitford’s text-based network analysis of Robert Southey’s Thalaba the Destroyer provides an excellent example of this. In addition to demonstrating the behavior of agile, well-connected nodes, the graph displays modules of nodes as units of analysis (Wasserman and Faust, 1994: 4).
Genetic Polymorphism on the Pharmacokinetics and Pharmacodynamics of Platelet-derived Growth Factor Receptor (PDGFR) Kinase Inhibitors.

BACKGROUND Platelet-derived Growth Factor Receptor (PDGFR) is a kind of Receptor Tyrosine Kinases (RTKs). PDGFR Tyrosine Kinase Inhibitors (TKIs) which are small molecule inhibitors targeting PDGFR prevent and block cell proliferation signal transduction pathways. Recently, there have been 11 TKIs (including imatinib, sunitinib, regorafenib, sorafenib, pazopanib, axitinib, dasatinib, nilotinib, lenvatinib, cabozantinib and ponatinib) targeting PDGFR approved by FDA for the treatment of chronic myelogenous leukemia, gastrointestinal stromal tumors, renal cell carcinoma et al. Pharmacokinetics (PK) reflects the processes of drugs in body, while pharmacodynamics (PD) reflects the efficacy. Genetic polymorphisms of metabolizers and transporters contribute to highly inter-individual variability in PK and PD. This review aims to introduce the clinical applications, instruction and usage, PK, PD and pharmacogenetics of these PDGFR TKIs. METHODS In vivo and in vitro studies about PDGFR TKIs were searched from PubMed. Data and information were analyzed and summarized. RESULTS The overview of (1) general information on PDGFR kinase inhibitors; (2) PK parameters of PDGFR kinase inhibitors; (3) metabolic enzymes and transporters of PDGFR kinase inhibitors; (4) main drug interactions of PDGFR kinase inhibitors; (5) adverse events of PDGFR kinase inhibitors; and (6) genetic polymorphism on PK and PD of PDGFR kinase inhibitors, was exhibited and discussed in this review. CONCLUSION This review summarized the general information, PK, metabolic enzymes and transporters, main drug interactions, adverse events and pharmacogenetics of FDA approved PDGFR TKIs. Studies showed that Single nucleotide polymorphisms of metabolic enzymes and transporters had influence on the PK and PD of PDGFR TKIs.
Effects of flanking regions on HDV cotranscriptional folding kinetics

Hepatitis delta virus (HDV) ribozyme performs the self-cleavage activity through folding to a double pseudoknot structure. The folding of functional RNA structures is often coupled with the transcription process. In this work, we developed a new approach for predicting the cotranscriptional folding kinetics of RNA secondary structures with pseudoknots. We theoretically studied the cotranscriptional folding behavior of the 99-nucleotide (nt) HDV sequence, two upstream flanking sequences, and one downstream flanking sequence. During transcription, the 99-nt HDV can effectively avoid the trap intermediates and quickly fold to the cleavage-active state. It is different from its refolding kinetics, which folds into an intermediate trap state. For all the sequences, the ribozyme regions (from 1 to 73) all fold to the same structure during transcription. However, the existence of the 30-nt upstream flanking sequence can inhibit the ribozyme region folding into the active native state through forming an alternative helix Alt1 with the segments 70–90. The longer upstream flanking sequence of 54 nt itself forms a stable hairpin structure, which sequesters the formation of the Alt1 helix and leads to rapid formation of the cleavage-active structure. Although the 55-nt downstream flanking sequence could invade the already folded active structure during transcription by forming a more stable helix with the ribozyme region, the slow transition rate could keep the structure in the cleavage-active structure to perform the activity.
Effectiveness and feasibility of Socratic feedback to increase awareness of deficits in patients with acquired brain injury: Four single-case experimental design (SCED) studies

ABSTRACT Objective: To investigate the effectiveness and feasibility of a Socratic feedback programme to improve awareness of deficits in patients with acquired brain injury (ABI). Setting: Rehabilitation centre. Participants: Four patients with ABI with awareness problems. Design: A series of single-case experimental design studies with random intervention starting points (A–B + maintenance design). Main measures: Rate of trainer-feedback and self-control behaviour on everyday tasks, patient competency rating scale (PCRS), self-regulating skills interview (SRSI), hospital anxiety and depression scale. Results: All patients needed less trainer feedback, the change was significant in 3 out of 4. One patient increased in overt self-corrective behaviour. SRSI performance increased in all patients (medium to strong effect size), and PCRS performance increased in two patients (medium and strong effect size). Mood and anxiety levels were elevated in one patient at the beginning of the training and decreased to normal levels at the end of the training. The feasibility of the programme was scored 9 out of 10. Conclusions: The Socratic feedback method is a promising intervention for improving awareness of deficits in patients with ABI. Controlled studies with larger populations are needed to draw more solid conclusions about the effect of this method.
Typology of phase transitions in Bayesian inference problems

Many inference problems undergo phase transitions as a function of the signal-to-noise ratio, a prominent example of this phenomenon being found in the stochastic block model (SBM) that generates a random graph with a hidden community structure. Some of these phase transitions affect the information-theoretic optimal (but possibly computationally expensive) estimation procedure, others concern the behavior of efficient iterative algorithms. A computational gap opens when the phase transitions for these two aspects do not coincide, leading to a hard phase in which optimal inference is computationally challenging. In this paper we refine this description in two ways. From a qualitative perspective, we emphasize the existence of more generic phase diagrams with a hybrid-hard phase, in which it is computationally easy to reach a nontrivial inference accuracy but computationally hard to match the information-theoretic optimal one. We support this discussion by quantitative expansions of the functional cavity equations that describe inference problems on sparse graphs, around their trivial solution. These expansions shed light on the existence of hybrid-hard phases, for a large class of planted constraint satisfaction problems, and on the question of the tightness of the Kesten-Stigum (KS) bound for the associated tree reconstruction problem. Our results show that the instability of the trivial fixed point is not generic evidence for the Bayes optimality of the message-passing algorithms. We clarify in particular the status of the symmetric SBM with four communities and of the tree reconstruction of the associated Potts model: In the assortative (ferromagnetic) case the KS bound is always tight, whereas in the disassortative (antiferromagnetic) case we exhibit an explicit criterion involving the degree distribution that separates a large-degree regime where the KS bound is tight and a low-degree regime where it is not. We also investigate the SBM with two communities of different sizes, also known as the asymmetric Ising model, and describe quantitatively its computational gap as a function of its asymmetry, as well as a version of the SBM with two groups of q_{1} and q_{2} communities. We complement this study with numerical simulations of the belief propagation iterative algorithm, confirming that its behavior on large samples is well described by the cavity method.
GeneExpressScore Signature: a robust prognostic and predictive classifier in gastric cancer

Although several prognostic signatures have been developed for gastric cancer (GC), the utility of these tools is limited in clinical practice due to lack of validation with large and multiple independent cohorts, or lack of a statistical test to determine the robustness of the predictive models. Here, a prognostic signature was constructed using a least absolute shrinkage and selection operator (LASSO) Cox regression model and a training dataset with 300 GC patients. The signature was verified in three independent datasets with a total of 658 tumors across multiplatforms. A nomogram based on the signature was built to predict disease‐free survival (DFS). Based on the LASSO model, we created a GeneExpressScore signature (GESGC) classifier comprised of eight mRNA. With this classifier patients could be divided into two subgroups with distinctive prognoses [hazard ratio (HR) = 4.00, 95% confidence interval (CI) = 2.41–6.66, P < 0.0001]. The prognostic value was consistently validated in three independent datasets. Interestingly, the high‐GESGC group was associated with invasion, microsatellite stable/epithelial–mesenchymal transition (MSS/EMT), and genomically stable (GS) subtypes. The predictive accuracy of GESGC also outperformed five previously published signatures. Finally, a well‐performed nomogram integrating the GESGC and four clinicopathological factors was generated to predict 3‐ and 5‐year DFS. In summary, we describe an eight‐mRNA‐based signature, GESGC, as a predictive model for disease progression in GC. The robustness of this signature was validated across patient series, populations, and multiplatform datasets.
Collocations and Network Structure Provide Insights to Functional Elements of Adaptive Capacity

Decades of field research have identified numerous characteristics and conditions, so-called “determinants,” such as education, wealth, social networks, government transparency, gender, and riskcommunication (Brooks et al. 2005; Smit & Wandel 2006; Tol & Yohe 2007), that affect the ability of individuals and groups to prepare for and respond to the effects of climate change. But why these particular determinants and how do they affect our capacity to adapt? We apply methods from computational text analysis (Sinclair 1991) and network analysis (Brandes 2001; Blondel et al. 2008) to offer an innovative approach to understanding the concept of adaptive capacity. Computational analyses allow us to reveal the unconscious rhetoric of adaptive capacity that illuminates how determinants are interconnected and how they might work to build adaptive capacity. These patterns are not stated or visible in a single study but emerge from a field-wide analysis. Results depict a concept map of adaptive capacity that operationalize the academic discourse and highlights points of convergence and divergence to inform future research.
Risk factors for marital violence among treatment seeking

The stereotype of the "drunken bum" wife abuser has a long history in American culture. U.S. population surveys document a positive correlation between alcohol consumption levels and marital violence. In this study risk factors for marital violence among treatment seeking male alcoholics were examined. Subjects were couples (N=107) who had a newly abstinent husband entering treatment in the Counseling for Alcoholics' Marriages Project. Subjects were divided into aggressive and nonaggressive categories based on responses to the Conflict Tactics Scale. Drinking patterns, drinking location, antisocial and other aggressive behavior, severity of alcohol problems, family drinking history, motivations for drinking and beliefs about alcohol, marital disharmony and conflict, and demographic variables were assessed. Results indicated maritally aggressive alcoholics (N=71) were different from nonaggressive alcoholics (N=36) in their drinking patterns (more likely to have an arrest history and higher verbal aggression levels), alcohol problem severity (earlier problem onset and greater problem severity), family history (more alcohol problems among male biological relatives and less maternal use), beliefs about alcohol (less confidence in their ability to manage interpersonal conflict without drinking and stronger beliefs that alcohol causes marital problems), and demographics (younger age and shorter length of marriage). Surprisingly, extent of marital dissatisfaction did not distinguish the two groups. (Author/ABL) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. *********************************************************************** Factors Associated with Marital Aggression 1 Factors Associated with Marital Aggression in Mala Alcoholics Christopher M. Murphy University of Maryland Baltimore County and Timothy J. O'Farrell Veterans Affairs Medical Center, Brockton, MA and Harvard Medical School Presented at the Association for the Advancement of Behavior Therapy, Bostcn, MA, November, 1992. U.S. DEPARTMENT OF EDUCATION Oare0Educahooa.Resea,c1,aod,o,caovea"em EDUCATIONAL RESOURCES INFORMATION CENTER ERIC, Th.s document has Deer, eorrduced as , ec e.ve0 1,0, the peson e' o,gan. /. 31.0r 0.V1. 31,19.1 P.A. "0,ChangeSN]. [Wer,,ailv,e,Nye, W,Odurhon(1,,a,l, P(1i n I s Of vice. or op,ocos stated (,.5 CM men? do not "et essarIv er,ese,,I nt6ra OE RI 0051,0" o, oc,cr PE.RMIS',UN fiE PRUDLICE MATEi-? IAl HA', BEEN ,:04ANTt U 8) Lkzvviyd.
A cross-language co-word network comparison of Buddhist literature in Digital Library and Museum of Buddhist study

This paper reports a co-words domain analysis of Buddhism literature collected by DLMBS (Digital Library and Museum of Buddhist studies) at National Taiwan University. Established in 1995, the DLMBS is one of the most comprehensive online repository of Buddhist research materials. It currently contains over 400 thousand records of books, research papers, theses and dissertations in 45 languages and digitized Buddhist scriptures. A controlled vocabulary, which is in five languages, including Chinese, English, Japanese, German, and French, was used to help users search DLMBS’s bibliographic database. By using cooccurrence data of author assigned keywords in the bibliographic records, this study attempts to generate co-word networks in three different languages, Chinese, English, and Japanese, to compare regional focuses on Buddhist studies. Co-words analysis has been shown to be effective in mapping the intellectual structure of disciplines (He, 1999; Leydesdroff, 1989). While it has been widely used in the domains of sciences and technologies (e.g. Buitelaar, Bordea, & Coughlan, 2014; Ding, Chowdhury, & Foo, 2001; Bhattacharya & Basu,1998; Looze, & Lemarie, 1997; Peters & van Raan, 1993a, 1993b; Courtial, 1994; Tijssen, 1992; Callon, Courtial, & Laville, 1991; Rip & Courtial, 1984), to the best our knowledge, it has so far not been applied to humanities. Part of the advantage of using co-word in sciences and technologies is the highly codified subject languages, therefore a higher degree of consistency between concepts and terms in these fields. We believe that a cross-language co-word analysis of Buddhist studies literature would be a worthwhile endeavor for a couple of reasons: Firstly, it has been pointed out that there has been a wide variety of methods, perspectives and subject matters within the international communities of Buddhist studies. The heterogeneity of its scholarships can be partly traced to their geographic roots (Cabezón, 1995). It is therefore interesting to empirically study whether and how the intellectual structures reflected in the published literatures in these language communities differ from one another. A comparison of the intellectual structures can shed light on knowledge interests shared and distinct in these three language communities. From the methodological plain, co-word analysis also provides a viable alternative to citationbased network analysis in humanities where the citation structure is known to be much sparser than in sciences and technologies.
MiR-125b blocks Bax/Cytochrome C/Caspase-3 apoptotic signaling pathway in rat models of cerebral ischemia-reperfusion injury by targeting p53

ABSTRACT Objective: To explore the potential effect of miR-125b on p53-mediated regulation of Bax/Cytochrome C/Caspase-3 apoptotic signaling pathway in rats with cerebral ischemia-reperfusion (CIR) injury. Methods: Sprague-Dawley (SD) rats were used to conduct CIR injury and injected with miR-125b mimic/inhibitor or p53 inhibitor (Pifithrin-α, PFT-α). Dual-luciferase reporter gene assay was used to analyze the targeting relationship between miR-125b and p53. Longa scoring and Triphenyl tetrazolinm chloride (TTC) staining were used to test the neurologic function and determine infarct size, respectively. Hematoxylin-eosin (HE) and Nissl’s stainings were conducted to observe the morphology of cortical neurons. Neuronal nuclei (NeuN) expression was detected by immunohistochemical staining. QRT-PCR was performed to detect the expressions of miR-125b and p53. TUNEL staining and Western blotting was used to determine neuronal apoptosis and expressions of Bax/Cytochrome C/Caspase-3 signaling pathway-related proteins, respectively. Results: Our results showed that miR-125b could directly target p53. As observed, overexpression of miR-125b could obviously reduce the neurological score, infarct size, and brain water content after CIR in rats, which also improved the morphology of cortical neurons, increased the number of neurons, reduced neuronal apoptosis, and inhibited the expressions of Bax/Cytochrome C/Caspase-3 pathway. Moreover,the similar results were observed in rats with CIR after injected with PFT-α. But no significant differences in each index were found in CIR group and CIR + anti-miR-125b + PFT-α group. Conclusion: MiR-125b exerts protective effects on CIR injury through inhibition of Bax/Cytochrome C/Caspase-3signaling pathway via targeting p53, which is likely to be a promising treatment for CIR. Abbreviations: 3’–UTR: 3–untranslated region; CIR: cerebral ischemia–reperfusion; CIS: cerebral ischemic stroke; PFT–α: Pifithrin–α; PVDF: polyvinylidene fluoride; SD: Sprague–Dawley; TBST: tris buffered saline with tween. TTC staining: Triphenyl tetrazolinm chloride staining; TUNEL: Terminal deoxynucleotidyl transferase–mediated dUTP–biotin nick end labeling.
Fixed point implementation for parameters extraction in a digital predistorter using adaptive algorithms

In this paper, the parameters extraction from the Volterra series to analyze the performance of a Digital Predistorter (DPD), for the Power Amplifier (PA) with memory, is introduced in two different ways: (1) different numerical methods for the parameters extraction and (2) the fixed point numerical format implementation for this numerical method. The parameters in the Volterra Model are typically calculated based on the mean square error criteria. In this paper, we present some alternatives to reduce the complexity, number of operations, and a PA linearization time ,with DPD dealing with OFDM signals. The simulation results show that with the Volterra model, both the LMS and the VSS algorithms are faster and more effective to calculate the parameters and mantain their convergence properties for a 32-bits implementation.
Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits in Drosophila melanogaster

Traits with a common genetic basis frequently display correlated phenotypic responses to selection or environmental conditions. In Drosophila melanogaster, pigmentation of the abdomen and a trident‐shaped region on the thorax are genetically correlated. Here, we used a pooled replicated genomewide association approach (Pool‐GWAS) to identify the genetic basis of variation in thoracic trident pigmentation in two Drosophila melanogaster populations. We confirmed the previously reported large effect of ebony and the association of the cosmopolitan inversion In(3R)Payne. For the first time, we identified tan as another major locus contributing to variation in trident pigmentation. Intriguingly, the regulatory variants of tan that were most strongly associated with female abdominal pigmentation also showed a strong association with trident pigmentation. We validated this common genetic basis in transgenic assays and found qualitatively similar effects on trident and abdominal pigmentation. Further work is required to determine whether this genetic correlation is favoured by natural selection or reflects a neutral by‐product of a shared regulatory architecture.