Miracle-dz/UniFAR-FTUs huggingface dataset:
The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress

Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 ARF genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and Arabidopsis suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from Arabidopsis. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in MaARF genes ranged from 5 to 21, suggesting large variation amongst banana ARF genes. The comprehensive expression profiles of MaARF genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MaARF genes for further functional assays in planta. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of MaARF gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.
Distributed Response Time Analysis of GSPN Models with MapReduce

Generalized stochastic Petri nets (GSPNs) are widely used in the performance analysis of computer and communications systems. Response time densities and quantiles are often key outputs of such analysis. These can be extracted from a GSPN’s underlying semi-Markov process using a method based on numerical Laplace transform inversion. This method typically requires the solution of thousands of systems of complex linear equations, each of rank n, where n is the number of states in the model. For large models substantial processing power is needed and the computation must therefore be distributed. In this paper we describe the implementation of a response time analysis module for the Platform Independent Petri net Editor (PIPE2) which interfaces with Hadoop, an open-source implementation of Google’s MapReduce distributed programming environment, to provide distributed calculation of response time densities in GSPN models. The software is validated with results calculated analytically as well as simulated results for larger models. Excellent scalability is shown.
Polymer rheology simulations at the meso- and macroscopic scale

We show that simulations of polymer rheology at a fluctuating mesoscopic scale and at the macroscopic scale where flow instabilities occur can be achieved at the same time with dissipative particle dynamics (DPD) technique. We model the viscoelasticity of polymer liquids by introducing a finite fraction of dumbbells in the standard DPD fluid. The stretching and tumbling statistics of these dumbbells is in agreement with what is known for isolated polymers in shear flows. At the same time, the model exhibits behaviour reminiscent of drag reduction in the turbulent state: as the polymer fraction increases, the onset of turbulence in plane Couette flow is pushed to higher Reynolds numbers. The method opens up the possibility to model non-trivial rheological conditions with ensuing coarse-grained polymer statistics.
Development and implementation of fiducial markers for vocal tract MRI imaging and speech articulatory modelling

MRI allows characterizing the shape and position of speech articulators, but not tracking flesh points, since there are no physiological landmarks reliably associated with the highly deformable tissues of these articulators. This information is, however, interesting for studying the biomechanical properties of these organs as well as for modelling the relations between measurement modalities such as MRI and electromagnetic articulography. We have therefore attached fiducial markers made of MRI-visible polymers to a speaker's articulators, and recorded a corpus of MRI midsagittal images. We then determined and analyzed the articulators' contours and the markers' centre coordinates. We found that the "apparent sliding" of markers with respect to lips and tongue contours ranges between 0.6 and 1.5 cm. Specifically, the curvilinear distances between two tongue flesh points relative to the total length varied up to about ±20%, confirming a non longitudinal elasticity of the contours. However, we have also found that the markers and jaw coordinates can predict the articulators' contours with a variance explanation of about 85 %, and an RMS reconstruction error between 0.08 and 0.15 cm, compared with 74 to 95 % of variance and 0.07 to 0.14 cm of RMS error for the original articulatory models.
Customers' International Online Trust - Insights from Focus Group Interviews

While scholars have made an extensive research contribution on the field of customers' online trust towards domestic retailers, customers' international online trust has not yet attracted researchers' attention. Following the extensive expansion of customers' online purchasing the purpose of this paper is to gain a deeper knowledge of the multidimensionality of trust in customer international online trust. In this paper trust is discussed and explored on three analytical levels: trust towards country of origin (COO), trust towards retailers, and retailers' website. Using data from five focus group interviews, the findings show that in an international online context the multidimensionality of trust is even more complex than previously assumed. At first sight the study reveals the importance of trust toward the COO of the retailer, the retailer's website, and the retailer itself. But interestingly the study revealed that third parties had a significant impact on customer international online trust and decreased the impact of customers' trust towards COO, websites, and retailers.
Prevention of Experimental Cerebral Vasospasm by Intracranial Delivery of a Nitric Oxide Donor From a Controlled-Release Polymer: Toxicity and Efficacy Studies in Rabbits and Rats

Background and Purpose— A reduction in the local availability of nitric oxide (NO) may play a role in the etiology of chronic cerebral vasospasm after subarachnoid hemorrhage (SAH). We investigated the toxicity and efficacy of a locally delivered NO donor from a controlled-release polymer in preventing experimental cerebral vasospasm in rats and rabbits, respectively. Methods— Diethylenetriamine/NO (DETA/NO) was incorporated into controlled release ethylene-vinyl acetate (EVAc) polymers. Twenty-eight rats were used in a dose-escalation toxicity study to establish a maximally tolerated dose of DETA/NO-EVAc polymer. In the efficacy experiment, 20 rabbits were assigned to 4 experimental groups (n=5 per group): sham operation; SAH only; SAH+empty EVAc polymer; and SAH+DETA/NO-EVAc polymer. Treatment was initiated 30 minutes after blood deposition. Basilar artery lumen patency was assessed 72 hours after hemorrhage to evaluate the efficacy of DETA/NO in preventing cerebral vasospasm. Results— In the toxicity study, a dose of 3.4 mg/kg was identified as the LD20 (dose with 20% mortality during the study period) of this DETA/NO formulation. Brain histology revealed hemorrhage and ischemic changes at the implantation site associated with high concentrations of DETA/NO. In the efficacy study, treatment with DETA/NO-EVAc polymer resulted in a significant decrease in basilar artery vasospasm compared with no treatment (93.0±4.9% versus 71.4±11.9%;P =0.035) or compared with treatment with blank EVAc polymer (93.0±4.9% versus 73.2±6.4%;P =0.003). Conclusions— Local delivery of DETA/NO prevents vasospasm in the rabbit basilar artery. Local delivery of DETA/NO via polymers is a safe and effective strategy for preventing cerebral vasospasm after SAH in this model.
ViralZone: a knowledge resource to understand virus diversity

The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
Evaluating Agent-Oriented Software Engineering Methodologies

This paper contributes to the evolution of Agent Oriented Software Engineering Approach (AOSE) by proposing a new framework called Multilevel Features Analysis Framework (MFAF) for software evaluation in general and Role-Based AOSE methodologies evaluation in particular. MFAF is a generalpurpose framework that can be adopted and adapted to evaluate software-related products (e.g., programming languages, software engineering methodologies, software development tools, Interaction communications protocols, etc.). This evaluation framework is applied to a number of role-based AOSE methodologies. In this paper we also document the results of applying MFAF on the CASSIOPEIA method. KeywordsAOSE Methodologies Evaluation , Comparing Agent Development Methodologies, AOSE.
Aripiprazole-induced tardive dyskinesia treated with quetiapine: a case report

Tomruk NB, Saatcioglu O, Yildizhan E, Alpay N. Aripiprazole-induced tardive dyskinesia treated with quetiapine: a case report. Background: Tardive dyskinesia (TD) is a serious, potentially irreversible side effect of antipsychotics. Although the risk is smaller, atypical antipsychotics still pose a risk. Aripiprazole is an atypical antipsychotic with a unique mechanism of action. It has a partial agonistic effect on the presynaptic D2 dopamine autoreceptor and antagonistic effect at postsynaptic D2 receptors. Method: There have been a few case reports of aripiprazole-induced TD. A case of aripiprazole-induced TD successfully treated with another atypical antipsychotic, quetiapine, is described and discussed in line with the recent literature. Results: TD showed rapid improvement with discontinuation of aripiprazole and initiation of quetiapine. Conclusion: Further studies are needed to ascertain the differential effects and side effects of second-generation antipsychotics in terms of TD.
Love-related changes in the brain: a resting-state functional magnetic resonance imaging study

Romantic love is a motivational state associated with a desire to enter or maintain a close relationship with a specific other person. Functional magnetic resonance imaging (fMRI) studies have found activation increases in brain regions involved in the processing of reward, motivation and emotion regulation, when romantic lovers view photographs of their partners. However, not much is known about whether romantic love affects the brain’s functional architecture during rest. In the present study, resting state functional magnetic resonance imaging (rsfMRI) data was collected to compare the regional homogeneity (ReHo) and functional connectivity (FC) across an “in-love” group (LG, N = 34, currently intensely in love), an “ended-love” group (ELG, N = 34, ended romantic relationship recently), and a “single” group (SG, N = 32, never fallen in love). Results show that: (1) ReHo of the left dorsal anterior cingulate cortex (dACC) was significantly increased in the LG (in comparison to the ELG and the SG); (2) ReHo of the left dACC was positively correlated with length of time in love in the LG, and negatively correlated with the lovelorn duration since breakup in the ELG; (3) FC within the reward, motivation, and emotion regulation network (dACC, insula, caudate, amygdala, and nucleus accumbens) as well as FC in the social cognition network [temporo-parietal junction (TPJ), posterior cingulate cortex (PCC), medial prefrontal cortex (MPFC), inferior parietal, precuneus, and temporal lobe] was significantly increased in the LG (in comparison to the ELG and SG); (4) in most regions within both networks FC was positively correlated with the duration of love in the LG but negatively correlated with the lovelorn duration of time since breakup in the ELG. This study provides first empirical evidence of love-related alterations in brain functional architecture. Furthermore, the results shed light on the underlying neural mechanisms of romantic love, and demonstrate the possibility of applying a resting-state fMRI approach for investigating romantic love.
Timed Efficient Stream Loss-Tolerant Authentication (TESLA): Multicast Source Authentication Transform Introduction

This document introduces Timed Efficient Stream Loss-tolerant Authentication (TESLA). TESLA allows all receivers to check the integrity and authenticate the source of each packet in multicast or broadcast data streams. TESLA requires no trust between receivers, uses low-cost operations per packet at both sender and receiver, can tolerate any level of loss without retransmissions, and requires no per-receiver state at the sender. TESLA can protect receivers against denial of service attacks in certain circumstances. Each receiver must be loosely time-synchronized with the source in order to verify messages, but otherwise receivers do not have to send any messages. TESLA alone cannot support non-repudiation of the data source to third parties. This informational document is intended to assist in writing standardizable and secure specifications for protocols based on TESLA in different contexts. This memo provides information for the Internet community.
DPARSF: A MATLAB Toolbox for “Pipeline” Data Analysis of Resting-State fMRI

Resting-state functional magnetic resonance imaging (fMRI) has attracted more and more attention because of its effectiveness, simplicity and non-invasiveness in exploration of the intrinsic functional architecture of the human brain. However, user-friendly toolbox for “pipeline” data analysis of resting-state fMRI is still lacking. Based on some functions in Statistical Parametric Mapping (SPM) and Resting-State fMRI Data Analysis Toolkit (REST), we have developed a MATLAB toolbox called Data Processing Assistant for Resting-State fMRI (DPARSF) for “pipeline” data analysis of resting-state fMRI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), and fractional ALFF. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest.
GLI1 regulates a novel neuropilin-2/alpha6beta1 integrin based autocrine pathway that contributes to breast cancer initiation

Repository Citation Goel HL, Pursell BM, Chang C, Shaw LM, Mao J, Simin K, Kumar P, Vander Kooi CW, Shultz LD, Greiner DL, Norum JH, Toftgard R, Kuperwasser C, Mercurio AM. (2013). GLI1 regulates a novel neuropilin-2/ alpha6beta1 integrin based autocrine pathway that contributes to breast cancer initiation. University of Massachusetts Medical School Faculty Publications. https://doi.org/10.1002/emmm.201202078. Retrieved from https://escholarship.umassmed. edu/faculty_pubs/109
Requirements for wireless sensor networks in order to achieve digital forensic readiness

The field of wireless sensor networking is a new and upcoming one and unfortunately still lacking as far as digital forensics is concerned. All communications between different nodes (also known as motes) are sent out in a broadcast fashion. These broadcasts make it quite difficult to capture data packets forensically whilst retaining their integrity and authenticity. This paper examines the differences between IEEE 802.15. 4 wireless sensor networks and IEEE 802.11x wireless networks when it comes to implementing digital forensic readiness within the network environment. It focuses on the differences in the communication protocol, proof of authenticity and integrity, time stamping, modification of the network after deployment and other differences between IEEE 802.15. 4 wireless sensor networks and IEEE 802.11x wireless networks. Each of these elements is discussed, after which a table is provided that shows the specific requirements to be taken into account when proposing digital forensic readiness in a wireless sensor network environment.
LEADERSHIP : NONWORK-RELATED ADVICE IN A WORK SETTING

Opinion leaders influence the decisions of others and play a significant role in disseminating information, specifically in the domain of e-commerce. Prior studies exploring the factors that affect a person‟s ability to influence others have been conducted in either a work setting [i.e. advice networks] or leisure setting (e.g. movie recommendation). However, it is common for these networks to interweave, for instance when a person asks for advice from work colleagues on a personal issue, like the purchase of a car. This suggests that there is a need to differentiate between the antecedents of opinion leadership that stem from one‟s position in the professional network and the antecedents that stem from personal characteristics associated with the specific non-work related advice [e.g. expertise in cars]. To explore how opinion leadership is determined in such multifaceted settings, we develop a theoretical framework of opinion leadership. The results from an empirical study of a movie advice task that was conducted in a professional setting, demonstrate that both movie-related trustworthiness and work-related centrality exert distinct effects on one's ability to influence others opinions regarding movies. Implications for theory and practice of e-commerce are discussed.
Unsupervised Multiresolution Segmentation for Images with Low Depth of Field

Unsupervised segmentation of images with low depth of field (DOF) is highly useful in various applications. This paper describes a novel multiresolution image segmentation algorithm for low DOF images. The algorithm is designed to separate a sharply focused object-of-interest from other foreground or background objects. The algorithm is fully automatic in that all parameters are image independent. A multi-scale approach based on high frequency wavelet coefficients and their statistics is used to perform context-dependent classification of individual blocks of the image. Unlike other edge-based approaches, our algorithm does not rely on the process of connecting object boundaries. The algorithm has achieved high accuracy when tested on more than 100 low DOF images, many with inhomogeneous foreground or background distractions. Compared with he state of the art algorithms, this new algorithm provides better accuracy at higher speed.
Tethering of Epidermal Growth Factor (EGF) to Beta Tricalcium Phosphate (βTCP) via Fusion to a High Affinity, Multimeric βTCP-Binding Peptide: Effects on Human Multipotent Stromal Cells/Connective Tissue Progenitors

Transplantation of freshly-aspirated autologous bone marrow, together with a scaffold, is a promising clinical alternative to harvest and transplantation of autologous bone for treatment of large defects. However, survival proliferation, and osteogenic differentiation of the marrow-resident stem and progenitor cells with osteogenic potential can be limited in large defects by the inflammatory microenvironment. Previous studies using EGF tethered to synthetic polymer substrates have demonstrated that surface-tethered EGF can protect human bone marrow-derived osteogenic stem and progenitor cells from pro-death inflammatory cues and enhance their proliferation without detriment to subsequent osteogenic differentiation. The objective of this study was to identify a facile means of tethering EGF to clinically-relevant βTCP scaffolds and to demonstrate the bioactivity of EGF tethered to βTCP using stimulation of the proliferative response of human bone-marrow derived mesenchymal stem cells (hBMSC) as a phenotypic metric. We used a phage display library and panned against βTCP and composites of βTCP with a degradable polyester biomaterial, together with orthogonal blocking schemes, to identify a 12-amino acid consensus binding peptide sequence, LLADTTHHRPWT, with high affinity for βTCP. When a single copy of this βTCP-binding peptide sequence was fused to EGF via a flexible peptide tether domain and expressed recombinantly in E. coli together with a maltose-binding domain to aid purification, the resulting fusion protein exhibited modest affinity for βTCP. However, a fusion protein containing a linear concatamer containing 10 repeats of the binding motif the resulting fusion protein showed high affinity stable binding to βTCP, with only 25% of the protein released after 7 days at 37oC. The fusion protein was bioactive, as assessed by its abilities to activate kinase signaling pathways downstream of the EGF receptor when presented in soluble form, and to enhance the proliferation of hBMSC when presented in tethered form on commercial βTCP bone regeneration scaffolds.
Magnetic resonance imaging of mediodorsal, pulvinar, and centromedian nuclei of the thalamus in patients with schizophrenia.

BACKGROUND Postmortem and magnetic resonance imaging (MRI) data have suggested volume reductions in the mediodorsal (MDN) and pulvinar nuclei (PUL) of the thalamus. The centromedian nucleus (CMN), important in attention and arousal, has not been previously studied with MRI. METHODS A sample of 41 patients with schizophrenia (32 men and 9 women) and 60 healthy volunteers (45 men and 15 women) underwent assessment with high-resolution 1.2-mm thick anatomical MRI. Images were differentiated to enhance the edges and outline of the whole thalamus, and the MDN, PUL, and CMN were outlined on all slices by a tracer masked to diagnostic status. RESULTS Significantly smaller volumes of the MDN and PUL were found in patients with schizophrenia compared with controls. Volume relative to brain size was reduced in all 3 nuclei; differences in relative reduction did not differ among the nuclei. The remainder of the thalamic volume (whole thalamus minus the volume of the 3 delineated nuclei) was not different between schizophrenic patients and controls, indicating that the volume reduction was specific to these nuclei. Volume relative to brain size was reduced in all 3 nuclei and remained significant when only patients who had never been exposed to neuroleptic medication (n = 15) were considered. For the MDN, women had larger relative volumes than men among controls, but men had larger volumes than women among schizophrenic patients. CONCLUSIONS Three association regions of the thalamus that have reciprocal connectivity to schizophrenia-associated regions of the cortex have significantly smaller volumes on MRI in patients with schizophrenia.