Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of a Novel I1781T Mutation and Other Mechanisms in Conferring Resistance to Acetyl-CoA Carboxylase Inhibiting Herbicides in a Black-Grass Population

Background Knowledge of the mechanisms of herbicide resistance is important for designing long term sustainable weed management strategies. Here, we have used an integrated biology and molecular approach to investigate the mechanisms of resistance to acetyl-CoA carboxylase inhibiting herbicides in a UK black-grass population (BG2). Methodology/Principal Findings Comparison between BG2 phenotypes using single discriminant rates of herbicides and genotypes based on ACCase gene sequencing showed that the I1781L, a novel I1781T, but not the W2027C mutations, were associated with resistance to cycloxydim. All plants were killed with clethodim and a few individuals containing the I1781L mutation were partially resistant to tepraloxydim. Whole plant dose response assays demonstrated that a single copy of the mutant T1781 allele conferred fourfold resistance levels to cycloxydim and clodinafop-propargyl. In contrast, the impact of the I1781T mutation was low (Rf = 1.6) and non-significant on pinoxaden. BG2 was also characterised by high levels of resistance, very likely non-target site based, to the two cereal selective herbicides clodinafop-propargyl and pinoxaden and not to the poorly metabolisable cyclohexanedione herbicides. Analysis of 480 plants from 40 cycloxydim resistant black grass populations from the UK using two very effective and high throughput dCAPS assays established for detecting any amino acid changes at the 1781 ACCase codon and for positively identifying the threonine residue, showed that the occurrence of the T1781 is extremely rare compared to the L1781 allele. Conclusion/Significance This study revealed a novel mutation at ACCase codon position 1781 and adequately assessed target site and non-target site mechanisms in conferring resistance to several ACCase herbicides in a black-grass population. It highlights that over time the level of suspected non-target site resistance to some cereal selective ACCase herbicides have in some instances surpassed that of target site resistance, including the one endowed by the most commonly encountered I1781L mutation.
On template-based reconstruction from a single view: Analytical solutions and proofs of well-posedness for developable, isometric and conformal surfaces

Recovering a deformable surface's 3D shape from a single view registered to a 3D template requires one to provide additional constraints. A recent approach has been to constrain the surface to deform quasi-isometrically. This is applicable to surfaces of materials such as paper and cloth. Current `closed-form' solutions solve a convex approximation of the original problem whereby the surface's depth is maximized under the isometry constraints (this is known as the maximum depth heuristic). No such convex approximation has yet been proposed for the conformal case. We give a unified problem formulation as a system of PDEs for developable, isometric and conformal surfaces that we solve analytically. This has important consequences. First, it gives the first analytical algorithms to solve this type of reconstruction problems. Second, it gives the first algorithms to solve for the exact constraints. Third, it allows us to study the well-posedness of this type of reconstruction: we establish that isometric surfaces can be reconstructed unambiguously and that conformal surfaces can be reconstructed up to a few discrete ambiguities and a global scale. In the latter case, the candidate solution surfaces are obtained analytically. Experimental results on simulated and real data show that our methods generally perform as well as or outperform state of the art approaches in terms of reconstruction accuracy.
Inter-User Interference in Body Sensor Networks: Preliminary Investigation and an Infrastructure-Based Solution

Inter-user interference is the interference in communication when several Body Sensor Networks (BSNs) operate in the same vicinity. As BSN users congregate in an area, interference due to concurrently communicating BSNs will increase, resulting in poor performance. In this paper, we conduct a preliminary investigation of the impact of inter-user interference and investigate its behavior with respect to parameters such as number of networks and the rates at which these networks communicate. Inter-user interference, is seen to reduce Packet Delivery Ratio by almost 35% in cases of 8 or more high-rate networks operating in the same location. We also propose a system to mitigate the adverse effects of inter-user interference. Our solution uses a fixed network infrastructure to monitor and identify BSNs that are likely to interfere with each other. The network then recommends changes to the BSN protocol to lessen interference between them. We also implement an instance of our system using a Wireless Sensor Network (WSN) infrastructure to reduce interference. The system is shown to significantly decrease the impact of inter-user interference.
Development of a spiral structure for an active catheter-overview of the spiral structure and its kinematic configuration

We propose a special structure for an active catheter: a spiral structure. It consists of a flexible belt on which actuators, sensors, and/or control units are built. The belt is spiraled or put spirally around flexible tube to work as a catheter. The actuators on one roll of the spiral move the next roll to realize the bending, twisting, and/or expanding motion of the catheter. With this method, minute and complicated actuators, sensors, and circuits can be precisely machined with very high density, fabricated and wired together in one continuous plane with silicon processes. The advantage of this method will be simple and high-density fabrication. In the paper, the overview and kinematic analysis of the spiral-structure active catheter are discussed and some types of active catheters are proposed.
Intralaminar Thalamic Nuclei Lesions: Widespread Impact on Dopamine Denervation‐Mediated Cellular Defects in the Rat Basal Ganglia

Intralaminar thalamic nuclei represent a major site of non-dopaminergic degeneration in Parkinson disease, but the impact of this degeneration on the pathophysiological functioning of basal ganglia remains unknown. To address this issue, we compared the effects of 6-hydroxydopamine-induced lesions of nigral dopamine neurons alone or combined with ibotenate-induced lesions of intralaminar thalamic neurons on markers of neuronal metabolic activity in the rat basal ganglia using in situ hybridization histochemistry. Thalamic lesions prevented most of the dopamine denervation-induced changes (i.e. the increases in mRNA levels of enkephalin and GAD67 in the striatum, of GAD67 in the globus pallidus and entopeduncular nucleus, and of cytochrome oxidase subunit-I in the subthalamic nucleus), but did not affect the downregulation of striatal substance P and upregulation of GAD67 in the substantia nigra pars reticulata. We also provide immunohistochemical evidence that thalamic lesions markedly decreased striatal expression of the vesicular glutamate transporter vGluT2, confirming the association of this transporter with the thalamic projections to the basal ganglia. Altogether, these data reveal a major antagonistic influence of thalamic and dopaminergic afferents onto the basal ganglia and suggest that degeneration of thalamic neurons in Parkinson disease may represent an important factor counteracting expression of the defects associated with the dopamine denervation.
Quality of reporting of modern randomized controlled trials in medical oncology: a systematic review.

BACKGROUND The Consolidated Standards of Reporting Trials (CONSORT) guidelines were developed in the mid-1990s for the explicit purpose of improving clinical trial reporting. However, there is little information regarding the adherence to CONSORT guidelines of recent publications of randomized controlled trials (RCTs) in oncology. METHODS All phase III RCTs published between 2005 and 2009 were reviewed using an 18-point overall quality score for reporting based on the 2001 CONSORT statement. Multivariable linear regression was used to identify features associated with improved reporting quality. To provide baseline data for future evaluations of reporting quality, RCTs were also assessed according to the 2010 revised CONSORT statement. All statistical tests were two-sided. RESULTS A total of 357 RCTs were reviewed. The mean 2001 overall quality score was 13.4 on a scale of 0-18, whereas the mean 2010 overall quality score was 19.3 on a scale of 0-27. The overall RCT reporting quality score improved by 0.21 points per year from 2005 to 2009. Poorly reported items included method used to generate the random allocation (adequately reported in 29% of trials), whether and how blinding was applied (41%), method of allocation concealment (51%), and participant flow (59%). High impact factor (IF, P = .003), recent publication date (P = .008), and geographic origin of RCTs (P = .003) were independent factors statistically significantly associated with higher reporting quality in a multivariable regression model. Sample size, tumor type, and positivity of trial results were not associated with higher reporting quality, whereas funding source and treatment type had a borderline statistically significant impact. CONCLUSION The results show that numerous items remained unreported for many trials. Thus, given the potential impact of poorly reported trials, oncology journals should require even stricter adherence to the CONSORT guidelines.
2 Language Modeling

My research interests lie in Machine Learning (ML) and its ap plications to Information Retrieval (IR), Information Extraction (IE) and Data Mining (DM). These applied areas ha ve historically been driven by empirical approaches. While these approaches have been quite successful in terms o f perf rmance, one of their major drawbacks is their lack of easy interpretability. It is my firm belief that machi ne learning approaches are a key towards solving some of the complex problems in text analysis and IR for the follow ing reasons: (i) ML techniques are theoretically well grounded, making them easily interpretable, (ii) the theor etical framework of ML techniques acts as a guidance for future researchers to build extensions to existing models a nd (iii) the theoretical foundation also makes the models generalizable and portable across different tasks and doma ins. In line with this philosophy, my research has thus far been ge ared towards advancing the state-of-the-art technology in the above mentioned areas using theoretically well motiv ated, machine learning based approaches. While staying within the confines of this broad objective, I consciously ma de n effort not to limit myself to any particular school of thought and retained the flexibility to build models in div erse frameworks such as discriminative and generative, supervised and unsupervised approaches. In the initial phase of my research as a graduate student at th e Center for Intelligent Information Retrieval, UMass, I was inspired by the elegant and simple Language Modeling (LM ) framework for IR. This led me to develop advanced models to overcome some of the deficiencies of existing model s in this framework [8, 9], which are described in section 2. Having gained some expertise in the LM framework, I realized there were some serious inadequacies in this approach especially in the web search context. To address th is i sue, I argued the case for using discriminative models such as SVMs for IR [6]. This work is briefly summarized in sect ion 3. In the last phase of my research as a graduate student, described in section 4, I took up the problem of findi ng an appropriate distribution for text as part of my thesis work and arrived at a novel variation of the Dirichlet distri bution called the Smoothed Dirichlet (SD) distribution. Intent on furthering my knowledge in theoretical machine le arning, I accepted a post doctoral fellowship offer from Prof. John Lafferty and Prof. William Cohen at Carnegie Mell on University (CMU). At CMU, I have had a chance to sharpen my ML skills not only through rigorous course work but also through the expert mentoring I received from Dr. Lafferty and Dr. Cohen. For the last one year, I have focus ed on unsupervised generative models for text called latent topic models, and applied them to mining patterns in l arge document collections [4]. This work is described in section 5. My future research plans, discussed in section 6, include bu ilding probabilistic graphical models for relational data such as blogs, scientific literature, etc., and a host of othe r applications.
A RULE-BASED APPROACH WITH METER ESTIMATION TO TEMPO ESTIMATION FOR AUDIO MUSIC

For audio music with time-varying meters, tempo estimation is a challenging task. This paper proposes several new low-level features of tempogram to determine pulse the classification of duple/triple meters, which can guide the determination of the overall tempo. After the judgment of meters, then we apply k-means clustering on tempo curve to perform tempo estimation. Index Terms – Tempo Estimation, Low-level Features, Tempogram, Tempo Curve, Duple/Triple Meter
Research on hierarchical image restoration of Chinese painting

This paper describes a new framework for Chinese paintings restoration using a hierarchy based approach. The framework involves three stages: layering phase, in which the painting is divided into two layers which are foreground layer and background layer; hierarchy restoration phase, in which foreground layer and background layer are restored separately based on different image restoration algorithm; synthesis phase, in which the two restored layers are composed to a complete painting.
Herbal help in Alzheimer's type of cognitive disorders: A Comprehensive Review

Alzheimer’s disease is the most frequent type of life threatening dementia which is characterized by oxidative stress and inflammation induced neuronal loss, impaired energy metabolism, and cholinergic deficits leading to severe cognitive impairments and other abnormal neuropsychiatric changes. Cure of cognitive disorders such as amnesia, attention deficit and Alzheimer’s disease is still a nightmare in the field of medicine and several nootropic agents are being used to improve memory, mood and behavior, but the resulting side effects associated with these agents have made their use limited. Indian system of medicine emphasizes use of herbs, nutraceuticals and life style changes for age related neurodegenerative disorders like Alzheimer’s disease. Current review sums up the plants that have shown the beneficial and encouraging results in treating ailments like Alzheimer’s disease.
Tamper Resistant Network Tracing

Raw network traces can be used to compromise the privacy of Internet users. For this reason, many ISPs are reluctant to collect network traces – they often regard possession of such traces as a liability. To mitigate this concern, anonymization techniques have been developed to protect user-identifying information. While most projects anonymize their traces as a post-processing step (i.e., offline), offline anonymization is insecure because raw data may still be exposed during the trace collection and anonymization steps. As an alternative, anonymization can be performed online, drastically reducing the privacy risks associated with storing raw data. Unfortunately, online anonymization is challenging in practice – data must be captured, reconstructed, analyzed, and anonymized at line speed. This paper presents a network tracing architecture that combines the performance benefits of offline anonymization with the privacy benefits of online anonymization. Our approach uses a virtual machine and an encrypted file system to protect the raw data allowing it to be securely anonymized offline. In this paper, we present our system’s design, and the implementation and evaluation of a simple prototype.
Reported Estimates of Adverse Pregnancy Outcomes among Women with and without Syphilis: A Systematic Review and Meta-Analysis

Background To estimate probability of adverse pregnancy outcomes (APOs) among women with and without syphilis through a systematic review of published literatures. Methodology/Principal Findings Chinese and English literatures were searched for studies assessing pregnancy outcomes in the presence of maternal syphilis through August 2013. The prevalence estimates were summarized and analyzed by meta-analysis. Fifty-four literatures involving 11398 syphilitic women and 43342 non-syphilitic women were included from 4187 records initially found. Among untreated mothers with syphilis, pooled estimates were 76.8% for all APOs, 36.0% for congenital syphilis, 23.2% for preterm, 23.4% for low birth weight, 26.4% for stillbirth or fetal loss, 14.9% for miscarriage and 16.2% for neonatal deaths. Among syphilitic mother receiving treatment only in the late trimester (>28 weeks), pooled estimates were 64.4% for APOs, 40.6% for congenital syphilis, 17.6% for preterm, 12.4% for low birth weight, and 21.3% for stillbirth or fetal loss. Among syphilitic mothers with high titers (≥1∶8), pooled estimates were 42.8% for all APOs, 25.8% for congenital syphilis, 15.1% for preterm, 9.4% for low birth weight, 14.6% for stillbirth or fetal loss and 16.0% for neonatal deaths. Among non-syphilitic mothers, the pooled estimates were 13.7% for all APOs, 7.2% for preterm birth, 4.5% for low birth weight, 3.7% for stillbirth or fetal loss, 2.3% for miscarriage and 2.0% for neonatal death. Begg's rank correlation test indicated little evidence of publication bias (P>0.10). Substantial heterogeneity was found across studies in the estimates of all adverse outcomes for both women with syphilis (I 2 = 93.9%; P<0.0001) and women without syphilis (I 2 = 94.8%; P<0.0001). Conclusions/Significance Syphilis continues to be an important cause of substantial perinatal morbidity and mortality, which reminds that policy-makers charged with resource allocation that the elimination of mother-to-child transmission of syphilis is a public health priority.
Science mapping the knowledge base on educational leadership and management in Africa, 1960–2018

ABSTRACT This review of research employed science mapping to analyse the intellectual structure of the knowledge base on educational leadership and management in Africa. The review analysed 645 Scopus-indexed documents on EDLM in Africa published between 1960 and 2018. Meta data associated with these documents were analysed using the VOSviewer software. The complementary use of citation and co-citation analysis determined that 95% of the African literature in EDLM has been published since 2000. Geographical distribution of African scholarship was highly skewed with South African scholarship accounting for 74% of the corpus. Citations analyses also identified highly cited scholars and documents within this literature. Analysis of the intellectual structure of the African EDLM knowledge base identified four main Schools of Thought. Three of these were comprised primarily of Africa-based scholarship and determined to be 'distinctively African' in terms of topical foci. The ‘research front’ or most current topical trend in this literature concerns leadership for educational and social transformation. Recommendations are made for building capacity among African EDLM scholars as well as for next steps in advancing the literature.
Morphological structure in the Arabic mental lexicon: Parallels between standard and dialectal Arabic

The Arabic language is acquired by its native speakers both as a regional spoken Arabic dialect, acquired in early childhood as a first language, and as the more formal variety known as Modern Standard Arabic (MSA), typically acquired later in childhood. These varieties of Arabic show a range of linguistic similarities and differences. Since previous psycholinguistic research in Arabic has primarily used MSA, it remains to be established whether the same cognitive properties hold for the dialects. Here we focus on the morphological level, and ask whether roots and word patterns play similar or different roles in MSA and in the regional dialect known as Southern Tunisian Arabic (STA). In two intra-modal auditory-auditory priming experiments, we found similar results with strong priming effects for roots and patterns in both varieties. Despite differences in the timing and nature of the acquisition of MSA and STA, root and word pattern priming was clearly distinguishable from form-based and semantic-based priming in both varieties. The implication of these results for theories of Arabic diglossia and theories of morphological processing are discussed.
VEGFR2 Translocates to the Nucleus to Regulate Its Own Transcription

Vascular Endothelial Growth Factor Receptor-2 (VEGFR2) is the major mediator of the angiogenic effects of VEGF. In addition to its well known role as a membrane receptor that activates multiple signaling pathways, VEGFR2 also has a nuclear localization. However, what VEGFR2 does in the nucleus is still unknown. In the present report we show that, in endothelial cells, nuclear VEGFR2 interacts with several nuclear proteins, including the Sp1, a transcription factor that has been implicated in the regulation of genes needed for angiogenesis. By in vivo chromatin immunoprecipitation (ChIP) assays, we found that VEGFR2 binds to the Sp1-responsive region of the VEGFR2 proximal promoter. These results were confirmed by EMSA assays, using the same region of the VEGFR2 promoter. Importantly, we show that the VEGFR2 DNA binding is directly linked to the transcriptional activation of the VEGFR2 promoter. By reporter assays, we found that the region between -300/-116 relative to the transcription start site is essential to confer VEGFR2-dependent transcriptional activity. It was previously described that nuclear translocation of the VEGFR2 is dependent on its activation by VEGF. In agreement, we observed that the binding of VEGFR2 to DNA requires VEGF activation, being blocked by Bevacizumab and Sunitinib, two anti-angiogenic agents that inhibit VEGFR2 activation. Our findings demonstrate a new mechanism by which VEGFR2 activates its own promoter that could be involved in amplifying the angiogenic response.