Miracle-dz/UniFAR-FTUs huggingface dataset:
Salicylic Acid-Regulated Antioxidant Mechanisms and Gene Expression Enhance Rosemary Performance under Saline Conditions

Salinity stress as a major agricultural limiting factor may influence the chemical composition and bioactivity of Rosmarinus officinallis L. essential oils and leaf extracts. The application of salicylic acid (SA) hormone may alleviate salinity stress by modifying the chemical composition, gene expression and bioactivity of plant secondary metabolites. In this study, SA was applied to enhance salinity tolerance in R. officinallis. R. officinallis plants were subjected to saline water every 2 days (640, 2,000, and 4,000 ppm NaCl) and 4 biweekly sprays of SA at 0, 100, 200, and 300 ppm for 8 weeks. Simulated salinity reduced all vegetative growth parameters such as plant height, plant branches and fresh and dry weights. However, SA treatments significantly enhanced these plant growth and morphological traits under salinity stress. Salinity affected specific major essential oils components causing reductions in α-pinene, β-pinene, and cineole along with sharp increases in linalool, camphor, borneol, and verbenone. SA applications at 100–300 ppm largely reversed the effects of salinity. Interestingly, SA treatments mitigated salinity stress effects by increasing the total phenolic, chlorophyll, carbohydrates, and proline contents of leaves along with decline in sodium and chloride. Importantly, this study also proved that SA may stimulate the antioxidant enzymatic mechanism pathway including catalase (CAT), superoxide dismutase (SOD), and ascorbate peroxidase (APX) as well as increasing the non-enzymatic antioxidants such as free and total ascorbate in plants subjected to salinity. Quantitative real-time PCR analysis revealed that APX and 3 SOD genes showed higher levels in SA-treated rosemary under salinity stress, when compared to non-sprayed plants. Moreover, the expression level of selected genes conferring tolerance to salinity (bZIP62, DREB2, ERF3, and OLPb) were enhanced in SA-treated rosemary under salt stress, indicating that SA treatment resulted in the modulation of such genes expression which in turn enhanced rosemary tolerance to salinity stress.
The Pretreatment Neutrophil/Lymphocyte Ratio Is Associated with All-Cause Mortality in Black and White Patients with Non-metastatic Breast Cancer

The pretreatment neutrophil/lymphocyte ratio (NLR), derived from differential white blood cell counts, has been previously associated with poor prognosis in breast cancer. Little data exist, however, concerning this association in Black patients, who are known to have lower neutrophil counts than other racial groups. We conducted a retrospective cohort study of 236 Black and 225 non-Hispanic White breast cancer patients treated at a single institution. Neutrophil and lymphocyte counts were obtained from electronic medical records. Univariate and multivariate Cox regression models were used to determine hazard ratios (HRs) and 95% confidence intervals (95% CIs) of all-cause mortality and breast cancer-specific mortality in relation to pretreatment NLR. Overall, there were no associations between an elevated pretreatment NLR (NLR ≥3.7) and all-cause or breast cancer-specific mortality. Among patients without metastasis at the time of diagnosis, an elevated pretreatment NLR was independently associated with all-cause mortality, with a multivariable HR of 2.31 (95% CI: 1.10–4.86). Black patients had significantly lower NLR values than White patients, but there was no evidence suggesting racial heterogeneity of the prognostic utility of NLR. Pretreatment NLR was an independent predictor of all-cause mortality but not breast cancer-specific mortality in non-metastatic breast cancer patients.
Reference equations for the six-minute walk distance based on a Brazilian multicenter study

Background It is important to include large sample sizes and different factors that influence the six-minute walking distance (6MWD) in order to propose reference equations for the six-minute walking test (6MWT). Objective To evaluate the influence of anthropometric, demographic, and physiologic variables on the 6MWD of healthy subjects from different regions of Brazil to establish a reference equation for the Brazilian population. Method In a multicenter study, 617 healthy subjects performed two 6MWTs and had their weight, height, and body mass index (BMI) measured, as well as their physiologic responses to the test. Delta heart rate (∆HR), perceived effort, and peripheral oxygen saturation were calculated by the difference between the respective values at the end of the test minus the baseline value. Results Walking distance averaged 586±106m, 54m greater in male compared to female subjects (p<0.001). No differences were observed among the 6MWD from different regions. The quadratic regression analysis considering only anthropometric and demographic data explained 46% of the variability in the 6MWT (p<0.001) and derived the equation: 6MWDpred=890.46-(6.11×age)+(0.0345×age2)+(48.87×gender)-(4.87×BMI). A second model of stepwise multiple regression including ∆HR explained 62% of the variability (p<0.0001) and derived the equation: 6MWDpred=356.658-(2.303×age)+(36.648×gender)+(1.704×height)+(1.365×∆HR). Conclusion The equations proposed in this study, especially the second one, seem adequate to accurately predict the 6MWD for Brazilians.
Graph cut based image segmentation with connectivity priors

Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum.
A Family of Zero-Voltage-Transition Bridgeless Power-Factor-Correction Circuits With a Zero-Current-Switching Auxiliary Switch

A novel zero-voltage-transition high-efficiency bridgeless power-factor-correction (PFC) circuit with a zero-current-switching auxiliary switch was proposed, analyzed, and experimentally verified. An assist circuit, consisting of a resonant inductor, two blocking diodes, a clamping circuit, an autotransformer, and an auxiliary MOSFET switch, was used to reduce the turn-on switching loss of the two main switches of the bridgeless PFC circuit and the turn-off switching loss of the auxiliary switch. The soft commutation of the main switches is achieved without imposing an additional voltage stress on the main switches. Feedback gate-drive signals can be obtained by using an existing converter IC controller modified to fit the purpose. In this paper, a detailed description of the circuit operation will be given. Based on the analysis, the guidelines for the component selection are presented. A prototype of 100-kHz 600-W universal-line PFC bridgeless circuit was built to verify the proposed scheme. In addition, based on the same concept, a family of bridgeless PFC configuration was proposed.
Overview of DNA Repair in Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major

A wide variety of DNA lesions arise due to environmental agents, normal cellular metabolism, or intrinsic weaknesses in the chemical bonds of DNA. Diverse cellular mechanisms have evolved to maintain genome stability, including mechanisms to repair damaged DNA, to avoid the incorporation of modified nucleotides, and to tolerate lesions (translesion synthesis). Studies of the mechanisms related to DNA metabolism in trypanosomatids have been very limited. Together with recent experimental studies, the genome sequencing of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, has revealed interesting features of the DNA repair mechanism in these protozoan parasites, which will be reviewed here.
A multilingual embodied conversational agent for tutoring speech and language learning

Speech and language science and technology evolved under the assumption that speech was a solely auditory event. However, a burgeoning record of research findings reveals that our perception and understanding are influenced by a speaker's face and accompanying gestures, as well as the actual sound of the speech. Perceivers expertly use these multiple sources of information to identify and interpret the language input. Given the value of face-to-face interaction, our persistent goal has been to develop, evaluate, and apply animated agents to produce realistic and accurate speech. Baldi® is an accurate threedimensional animated talking head appropriately aligned with either synthesized or natural speech. Baldi has a realistic tongue and palate, which can be shown by making his skin transparent. Based on this research and technology, we have implemented computer-assisted speech and language tutors for children with language challenges and for all persons learning a second language. Our language-training program utilizes Baldi (or his likeness) as the conversational agent, who guides students through a variety of exercises designed to teach vocabulary and grammar, to improve speech articulation, and to develop linguistic and phonological awareness. We have also implemented multilingual agents, using a client/server architecture system. This system has been used to develop Bao, a Mandarin talker, which has been used in an initial training study for college students learning Mandarin as a new language. The results address the potential for using visible speech technology and pedagogy in language learning of both similar segments in the two languages and new speech segments in the new language. Although visible speech did not facilitate pronunciation learning relative to just auditory speech, we expect that a more prolonged training period would show an advantage of visible speech. Some of the advantages of the Baldi pedagogy and technology include the popularity and proven effectiveness of computers and embodied conversational agents, the perpetual availability of the program, and individualized instruction. The science and technology of Baldi holds great promise in language learning, dialog, human-machine interaction, education, and edutainment. Index Terms: Speech Animation, Language Learning
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

To better understand the role of alternative splicing, we conducted a large-scale analysis of reliable alternative isoforms of known human genes. Each isoform was classified according to its splice pattern and supporting evidence. We found that one-third of the alternative transcripts examined contain premature termination codons, and most persist even after rigorous filtering by multiple methods. These transcripts are apparent targets of nonsense-mediated mRNA decay (NMD), a surveillance mechanism that selectively degrades nonsense mRNAs. Several of these transcripts are from genes for which alternative splicing is known to regulate protein expression by generating alternate isoforms that are differentially subjected to NMD. We propose that regulated unproductive splicing and translation (RUST), through the coupling of alternative splicing and NMD, may be a pervasive, underappreciated means of regulating protein expression.
Array-Based FMR1 Sequencing and Deletion Analysis in Patients with a Fragile X Syndrome–Like Phenotype

Background Fragile X syndrome (FXS) is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null mutation, few conventional mutations have been identified at this locus, largely due to the clinical laboratory focus on the repeat tract. Methodology/Principal Findings To more thoroughly evaluate the frequency of conventional mutations in FXS-like patients, we used an array-based method to sequence FMR1 in 51 unrelated males exhibiting several features characteristic of FXS but with normal CGG-repeat tracts of FMR1. One patient was identified with a deletion in FMR1, but none of the patients were found to have other conventional mutations. Conclusions/Significance These data suggest that missense mutations in FMR1 are not a common cause of the FXS phenotype in patients who have normal-length CGG-repeat tracts. However, screening for small deletions of FMR1 may be of clinically utility.
A multimodal approach to initialisation for top-down speaker diarization of television shows

This paper presents a new multimodal approach to speaker diarization of TV show data. We hypothesize that the intraspeaker variation in visual information might be less than that in the corresponding acoustic information and therefore might be better suited to the task of speaker model initialisation. This is an acknowledged weakness of the computationally efficient top-down approach to speaker diarization that is used here. Experimental results show that a recently proposed approach to purification and the new multimodal approach to initialisation together deliver 22% and 17% relative improvements in diarization performance over the baseline system on independent development and evaluation datasets respectively.
Formulation and Evaluation of Ciprofloxacin Hydrochloride Soluble Ocular Drug Insert

Purpose: An attempt has been made in the present research to formulate soluble ocular inserts of ciprofloxacin hydrochloride to increase residence time and prolong drug release. Material and Methods: Drug matrices were prepared using natural polymer. Gelatin, a biodegradable polymer, was tried for the first time in the preparation of soluble ocular drug insert matrices. The inserts were then evaluated for their physicochemical parameters. The in vitro drug release studies were carried out using a bi-chambered donor receiver compartment model. In vivo drug release was carried out using rabbits as animal models. Results: Formulations CF4 and CF8, which showed controlled and prolonged in vitro drug release, were subjected to in vivo study. In vitro and in vivo correlation was found to be strong, revealing the efficacy of the formulation. Conclusion: Formulation CF8 was found promising, as it achieved the target of the present study.
Trans Fat Consumption and Aggression

Background Dietary trans fatty acids (dTFA) are primarily synthetic compounds that have been introduced only recently; little is known about their behavioral effects. dTFA inhibit production of omega-3 fatty acids, which experimentally have been shown to reduce aggression. Potential behavioral effects of dTFA merit investigation. We sought to determine whether dTFA are associated with aggression/irritability. Methodolgy/Prinicpal Findings We capitalized on baseline dietary and behavioral assessments in an existing clinical trial to analyze the relationship of dTFA to aggression. Of 1,018 broadly sampled baseline subjects, the 945 adult men and women who brought a completed dietary survey to their baseline visit are the target of this analysis. Subjects (seen 1999–2004) were not on lipid medications, and were without LDL-cholesterol extremes, diabetes, HIV, cancer or heart disease. Outcomes assessed adverse behaviors with impact on others: Overt Aggression Scale Modified-aggression subscale (primary behavioral endpoint); Life History of Aggression; Conflict Tactics Scale; and self-rated impatience and irritability. The association of dTFA to aggression was analyzed via regression and ordinal logit, unadjusted and adjusted for potential confounders (sex, age, education, alcohol, and smoking). Additional analyses stratified on sex, age, and ethnicity, and examined the prospective association. Greater dTFA were strongly significantly associated with greater aggression, with dTFA more consistently predictive than other assessed aggression predictors. The relationship was upheld with adjustment for confounders, was preserved across sex, age, and ethnicity strata, and held cross-sectionally and prospectively. Conclusions/Significance This study provides the first evidence linking dTFA with behavioral irritability and aggression. While confounding is always a concern in observational studies, factors including strength and consistency of association, biological gradient, temporality, and biological plausibility add weight to the prospect of a causal connection. Our results may have relevance to public policy determinations regarding dietary trans fats. Clinicaltrials.gov # NCT00330980
Tau Oligomers as Potential Targets for Alzheimer’s Diagnosis and Novel Drugs

A cumulative number of approaches have been carried out to elucidate the pathogenesis of Alzheimer’s disease (AD). Tangles formation has been identified as a major event involved in the neurodegenerative process, due to the conversion of either soluble peptides or oligomers into insoluble filaments. Most of recent studies share in common the observation that formation of tau oligomers and the subsequent pathological filaments arrays is a critical step in AD etiopathogenesis. Oligomeric tau species appear to be toxic for neuronal cells, and therefore appear as an appropriate target for the design of molecules that may control morphological and functional alterations leading to cognitive impairment. Thus, current therapeutic strategies are aimed at three major types of molecules: (1) inhibitors of protein kinases and phosphatases that modify tau and that may control neuronal degeneration, (2) methylene blue, and (3) natural phytocomplexes and polyphenolics compounds able to either inhibit the formation of tau filaments or disaggregate them. Only a few polyphenolic molecules have emerged to prevent tau aggregation. In this context, fulvic acid (FA), a humic substance, has potential protective activity cognitive impairment. In fact, formation of paired helical filaments in vitro, is inhibited by FA affecting the length of fibrils and their morphology.
Preparation and Support of Patients through the Transplant Process: Understanding the Recipients' Perspectives

Preparation for heart transplant commonly includes booklets, instructional videos, personalized teaching sessions, and mentorship. This paper explores heart transplant recipients' thoughts on their preparation and support through the transplant process. Twenty-five interviews were audio-/videotaped capturing voice and body language and transcribed verbatim. Coding addressed language, bodily gesture, volume, and tone in keeping with our visual methodology. Recipients reported that only someone who had a transplant truly understands the experience. As participants face illness and life-altering experiences, maintaining a positive attitude and hope is essential to coping well. Healthcare professionals provide ongoing care and reassurance about recipients' medical status. Mentors, family members, and close friends play vital roles in supporting recipients. Participants reported that only heart transplant recipients understood the experience, the hope, and ultimately the suffering associated with living with another persons' heart. Attention needs to be focused not solely on the use of teaching modalities, but also on the development of innovative support networks. This will promote patient and caregiver engagement in self-management. Enhancing clinicians' knowledge of the existential aspects of transplantation will provide them with a nuanced understanding of the patients' experience, which will ultimately enhance their ability to better prepare and support patients and their caregivers.
Determination of the Primary Molecular Target of 1,2,4-Triazole-Ciprofloxacin Hybrids

We have synthesized and examined the antibacterial activity, toxicity and affinity towards bacterial type II topoisomerases of a series of 1,2,4-triazole-ciprofloxacin hybrids. A number of these compounds displayed enhanced activity against Gram-positive and Gram-negative bacteria when compared to ciprofloxacin. The toxic concentrations of the obtained derivatives, evaluated on HEK-293 cells using MTT assay, were much higher than concentrations required to produce antibacterial effect. Finally, the results of enzymatic studies showed that the analyzed compounds demonstrated other preferences as regards primary and secondary molecular targets than ciprofloxacin.
Cognitive Processes Associated with Sequential Tool Use in New Caledonian Crows

Background Using tools to act on non-food objects—for example, to make other tools—is considered to be a hallmark of human intelligence, and may have been a crucial step in our evolution. One form of this behaviour, ‘sequential tool use’, has been observed in a number of non-human primates and even in one bird, the New Caledonian crow (Corvus moneduloides). While sequential tool use has often been interpreted as evidence for advanced cognitive abilities, such as planning and analogical reasoning, the behaviour itself can be underpinned by a range of different cognitive mechanisms, which have never been explicitly examined. Here, we present experiments that not only demonstrate new tool-using capabilities in New Caledonian crows, but allow examination of the extent to which crows understand the physical interactions involved. Methodology/Principal Findings In two experiments, we tested seven captive New Caledonian crows in six tasks requiring the use of up to three different tools in a sequence to retrieve food. Our study incorporated several novel features: (i) we tested crows on a three-tool problem (subjects were required to use a tool to retrieve a second tool, then use the second tool to retrieve a third one, and finally use the third one to reach for food); (ii) we presented tasks of different complexity in random rather than progressive order; (iii) we included a number of control conditions to test whether tool retrieval was goal-directed; and (iv) we manipulated the subjects' pre-testing experience. Five subjects successfully used tools in a sequence (four from their first trial), and four subjects repeatedly solved the three-tool condition. Sequential tool use did not require, but was enhanced by, pre-training on each element in the sequence (‘chaining’), an explanation that could not be ruled out in earlier studies. By analyzing tool choice, tool swapping and improvement over time, we show that successful subjects did not use a random probing strategy. However, we find no firm evidence to support previous claims that sequential tool use demonstrates analogical reasoning or human-like planning. Conclusions/Significance While the ability of subjects to use three tools in sequence reveals a competence beyond that observed in any other species, our study also emphasises the importance of parsimony in comparative cognitive science: seemingly intelligent behaviour can be achieved without the involvement of high-level mental faculties, and detailed analyses are necessary before accepting claims for complex cognitive abilities.