Miracle-dz/UniFAR-FTUs huggingface dataset:
An overlooked plant–parakeet mutualism counteracts human overharvesting on an endangered tree

The exponential growth of the human population often causes the overexploitation of resources and disruption of ecological interactions. Here, we propose that the antagonist effect of humans on exploited species might be alleviated with the advent of a second predator species. We focused on the complex interactions between an endangered conifer (Araucaria araucana) and two seed exploiters: the Austral parakeet (Enicognathus ferrugineus) and human seed collectors. We tested the importance of partial seed consumption by parakeets as an escape from human seed harvesting. Although parakeets frequently ate whole seeds, a substantial proportion of the seeds found under trees were only partially eaten and avoided by human seed collectors. These seeds germinated at a similar proportion but faster than intact seeds under laboratory conditions. Our results revealed an overlooked mutualism between parakeets and an endangered tree. Incomplete seed eating by parakeets, plus selection against these eaten seeds by humans, may enhance regeneration possibilities for this conifer species subject to human seed collection, turning the scale of the antagonism–mutualism continuum to the mutualistic side. In this context, parakeets might be providing an important service in those forests subject to human harvesting by allowing a fraction of seeds to escape human predation.
Atrophy of the parahippocampal gyrus is prominent in heart failure patients without dementia

The exacerbation of heart failure (HF) induces brain damage and cognitive impairment (CI), which frequently attenuates the effects of treatment. However, it is not clear whether HF patients without clinical dementia demonstrate increased risk of CI. We examined whether local atrophy in the parahippocampal gyrus, a potential predictor of CI, is prominent in HF patients without clinical dementia.
The biochemistry and molecular biology of chlorophyll breakdown

Chlorophyll breakdown is one of the most obvious signs of leaf senescence and fruit ripening. The resulting yellowing of leaves can be observed every autumn, and the color change of fruits indicates their ripening state. During these processes, chlorophyll is broken down in a multistep pathway, now termed the 'PAO/phyllobilin' pathway, acknowledging the core enzymatic breakdown step catalysed by pheophorbide a oxygenase, which determines the basic linear tetrapyrrole structure of the products of breakdown that are now called 'phyllobilins'. This review provides an update on the PAO/phyllobilin pathway, and focuses on recent biochemical and molecular progress in understanding phyllobilin-modifying reactions as the basis for phyllobilin diversity, on the evolutionary diversity of the pathway, and on the transcriptional regulation of the pathway genes.
Comparing the Validity of Self-Report and Urinalysis for Substance Use among Former Inmates in the Northeastern United States

ABSTRACT Background: Problems with self-reported drug use include difficulties with recall and recognition as well as the desire to respond to questions in a socially desirable manner. Various methods have been developed to improve and/or validate estimates based on direct questioning of individuals regarding their substance use. For this study, we were interested in validating self-reported use of: 1) tobacco, 2) marijuana, and 3) other substances (i.e., heroin, cocaine, opiates, oxycodone, benzodiazepines, methamphetamine, phencyclidine, and barbiturates) employing urinalysis among inmates who participated in a randomized controlled trial of a smoking abstinence intervention in a tobacco-free prison located in the northeastern United States. Methods: Two-hundred and seven men and women with a mean age of 34.9 (standard deviation = 9.0) completed questions regarding their substance use on a 7-day Timeline Follow-Back and provided urine specimens three weeks following prison release. Results: Self-reported tobacco and marijuana use were highly consistent with urine drug testing in terms of overall agreement and Kappa (93.7% and.804 for tobacco, respectively; and 90.3% and.804 for marijuana, respectively); however, consistency was much lower for other drug use grouped together (62.7% and.270). Discussion: Although some former inmates may not accurately report substance use, our findings indicate that they are in the minority, suggesting that self-report is valid for tobacco and marijuana use but much less so for other drugs grouped together. Future research should be conducted with a larger and more diverse sample of former inmates to establish the generalizability of our findings from this study.
Quenching-free fluorescence signal from plastic-fibres in proton dosimetry: understanding the influence of Čerenkov radiation

The origin of photons emitted in optical fibres under proton irradiation has been attributed to either entirely Čerenkov radiation or light consisting of fluorescence with a substantial amount of Čerenkov radiation. The source of the light emission is assessed in order to understand why the signal from optical fibres irradiated with protons is reportedly quenching-free. The present study uses the directional emittance of Čerenkov photons in 12 MeV and 20 MeV electron beams to validate a Monte Carlo model for simulating the emittance and transmission of Čerenkov radiation in optical fibres. We show that fewer than 0.01 Čerenkov photons are emitted and guided per 225 MeV proton penetrating the optical fibre, and that the Čerenkov signal in the optical fibre is completely negligible at the Bragg peak. Furthermore, on taking the emittance and guidance of both fluorescence and Čerenkov photons into account, it becomes evident that the reported quenching-free signal in PMMA-based optical fibres during proton irradiation is due to fluorescence.
Spike threshold dynamics in spinal motoneurons during scratching and swimming

Action potential threshold can vary depending on firing history and synaptic inputs. We used an ex vivo carapace–spinal cord preparation from adult turtles to study spike threshold dynamics in motoneurons during two distinct types of functional motor behaviour – fictive scratching and fictive swimming. The threshold potential depolarizes by about 10 mV within each burst of spikes generated during scratch and swim network activity and recovers between bursts to a slightly depolarized level. Slow synaptic integration resulting in a wave of membrane potential depolarization is the factor influencing the threshold potential within firing bursts during motor behaviours. Depolarization of the threshold potential decreases the excitability of motoneurons and may provide a mechanism for stabilization of the response of a motoneuron to intense synaptic inputs to maintain the motor commands within an optimal range for muscle activation.
Vascular smooth muscle cell durotaxis depends on extracellular matrix composition

Significance Many cell types have been observed to migrate toward stiffer regions of mechanical gradients in a process termed durotaxis. Tissue stiffness gradients are being discovered in an increasing number of diseases, including cancer and fibrotic diseases. However, the role of ECM composition, which often changes in diseased tissues with stiffness, in directing this behavior has not previously been investigated. To understand how stiffness gradients and changing matrix composition may affect cell migration in disease, we have designed a mechanical gradient platform that allows for independent control of absolute stiffness, gradient steepness, and ECM coating. We demonstrate that smooth muscle cells will undergo durotaxis on mechanical gradients coated with fibronectin but not laminin. Mechanical compliance has been demonstrated to be a key determinant of cell behavior, directing processes such as spreading, migration, and differentiation. Durotaxis, directional migration from softer to more stiff regions of a substrate, has been observed for a variety of cell types. Recent stiffness mapping experiments have shown that local changes in tissue stiffness in disease are often accompanied by an altered ECM composition in vivo. However, the importance of ECM composition in durotaxis has not yet been explored. To address this question, we have developed and characterized a polyacrylamide hydrogel culture platform featuring highly tunable gradients in mechanical stiffness. This feature, together with the ability to control ECM composition, allows us to isolate the effects of mechanical and biological signals on cell migratory behavior. Using this system, we have tracked vascular smooth muscle cell migration in vitro and quantitatively analyzed differences in cell migration as a function of ECM composition. Our results show that vascular smooth muscle cells undergo durotaxis on mechanical gradients coated with fibronectin but not on those coated with laminin. These findings indicate that the composition of the adhesion ligand is a critical determinant of a cell’s migratory response to mechanical gradients.
Novel nanoparticulate systems for lung cancer therapy: an updated review

Abstract Lung cancer is the leading cause of cancer-related deaths in the world. Conventional therapy for lung cancer is associated with lack of specificity and access to the normal cells resulting in cytotoxicity, reduced cellular uptake, drug resistance and rapid drug clearance from the body. The emergence of nanotechnology has revolutionized the treatment of lung cancer. The focus of nanotechnology is to target tumor cells with improved bioavailability and reduced toxicity. In the recent years, nanoparticulate systems have extensively been exploited in order to overcome the obstacles in treatment of lung cancer. Nanoparticulate systems have shown much potential for lung cancer therapy by gaining selective access to the tumor cells due to surface modifiability and smaller size. In this review, various novel nanoparticles (NPs) based formulations have been discussed in the treatment of lung cancer. Nanotechnology is expected to grow fast in future, and it will provide new avenues for the improved treatment of lung cancer. This review article also highlights the characteristics, recent advances in the designing of NPs and therapeutic outcomes.
Age-Based Differences in Task Switching Are Moderated by Executive Control Demands

Objectives Recent work has identified different aspects of executive function that may underlie cognitive changes associated with age. The current study used a multifactorial design to investigate age sensitivity in the ability to shift between different task sets and the interaction of this ability with several specific aspects of executive control. Method A large, well-characterized sample of younger (n = 40) and clinically healthy older (n = 51) adults completed a task switching paradigm in which 3 aspects of executive control were manipulated between subjects: a) sensorimotor demand (the number of distinct stimulus-response options); b) stimulus-level interference (i.e., flanker effects); and c) updating/monitoring (the frequency of task switches). Results Unique age-related deficits were observed for different aspects of local task switching performance costs and updating/monitoring, but not for interference. Sensorimotor demand was also an important additional factor that interacted with task switching performance. Discussion Our findings suggest that task switching, coupled with infrequent and unexpected transitions from one task set to another, in the context of high motoric demands, is particularly difficult for older adults.
The impact of construction and gentrification on an outdoor trans sex work environment: Violence, displacement and policing

The objective of this study was to investigate how environmental and structural changes to a trans outdoor work environment impacted sex workers in Vancouver, Canada. The issue of changes to the work area arose during qualitative interviews with 33 trans sex workers. In response, ethnographic walks that incorporated photography were undertaken with trans sex workers. Changes to the work environment were found to increase vulnerabilities to client violence, displace trans sex workers, and affect policing practices. Within a criminalized context, construction and gentrification enhanced vulnerabilities to violence and harassment from police and residents.
Hoffa Fragments in the Geriatric Distal Femur Fracture: Myth or Reality?

Background: Previous research reported the frequency of coronal plane (Hoffa) fractures in high-energy supracondylar femur fractures in a relatively young population. It is the purpose of this study to identify the frequency of coronal plane fractures seen in elderly patients. Methods: All patients over the age of 18 years treated for supracondylar femur fractures at 2 level I trauma centers were reviewed over a 4-year period. The patients were stratified (≥60 years and <60 years) and compared to determine differences in injury characteristics and fracture patterns with special attention to the prevalence of coronal plane fractures. Results: One hundred ten patients were identified with supracondylar femur fractures (12 Orthopaedic Trauma Association [OTA] 33A; 2 OTA 33B; 96 OTA 33C). Thirty-two of the 96 intercondylar fractures were in patients >60 years of age. The elderly group included a higher percentage of females (81% vs 36%, P = .0001) and was more likely to sustain their injury due to a fall (59% vs 19%, P = .0001). Coronal plane fractures were visualized on computed tomography scans in 56 (58%) of the 96 33C femur fractures. Forty-four percent of elderly patients sustained a coronal plane fracture compared with 66% of the younger cohort (P = .04). The percentage of open fractures (30% elderly vs 46%) was not significantly different between the 2 groups (P = .17). Conclusions: The occurrence rate of 44% in this study was higher than expected and is the first to provide this information in the elderly patients on this fracture. It is important that a high index of suspicion be maintained for the Hoffa fracture in all distal femur fractures, regardless of age or mechanism of injury.
Modelling security requirements through extending Scrum agile development framework

4 DEDICATION. 5 DECLARATION. 6 ACKNOWLEDGEMENTS. 7 PUBLICATIONS. 8 LIST OF APPREVIATIONS. 16 LIST OF FIGURES. 17 LIST OF TABLES. 19 CHAPTER ONE: INTRODUCTION. 22 1.
Novel Synthesis of Dual-Frequency RF Energy-Harvesting Rectifier Incorporating Coupled Lines

In this paper, a novel synthesis technique for dual-frequency rectifier for ambient RF energy harvesting is proposed. For the first time, a fully distributed version of dual-frequency resistance compression network (RCN) is introduced. The proposed RCN utilizes the dual- frequency characteristic of the c-type coupled lines terminated into real impedance. The design technique is fully analytical based on closed-form design equations. Extensive simulations have been carried out to illustrate the proposed idea. The obtained results outperform the earlier reported lumped element network and provides a minimum 10% improvement in the RF-to-DC conversion efficiency at -20 dBm input power. The proposed technique can potentially serve as a starting point for the dual-frequency RF rectifier design.
Identifying Actionable Information from Social Media for Better Government-Public Relationship

Recent years have witnessed a sudden growth of online social media (OSM). Among the various OSM sites, Twitter, an online micro-blogging website has attracted interest of millions of users who use it to access, publish and spread (share) news at a quick pace much faster than conventional news mediums. Latching on this trend, governments across the world have started using Twitter to communicate, engage with their citizens and increase their visibility and popularity. Social media makes it simpler and convenient for citizens to voice their opinions and reach out to a large section of people, and also for the government to listen to their grievances and concerns. While the data on Twitter is quite informative, it presents a challenge for analysis because it is disorganized and highly voluminous with high velocity. Every day, government accounts receive thousands of messages from the general public in the form of opinions, concerns, and grievances. It becomes an extremely troublesome task for the concerned ministries in the government, to manually filter out the irrelevant messages and respond to the genuine ones. In this paper, we attempt to address this problem by using learning algorithms to automatically classify the user generated messages as either actionable (those which can be acted upon by the government ministries) or non-actionable. We have considered eight supervised learning algorithms to classify the messages into actionable or non-actionable and compared their outcomes to determine the most effective learning algorithm. Our results indicate that random forest classifier gave the best results with an aggregate accuracy of more than 0.94 and an F-score of 0.94.
Alcohol addiction - the safety of available approved treatment options

ABSTRACT Introduction: Alcohol Use Disorders (AUD) is a leading cause of mortality and morbidity worldwide. At present disulfiram, naltrexone and acamprosate are approved for the treatment of AUD in U.S. and Europe. Nalmefene is approved in Europe and sodium oxybate is approved in Italy and Austria only. Baclofen received a ‘temporary recommendation for use’ in France. Areas covered: The safety of the above mentioned medications on liver, digestive system, kidney function, nervous system, pregnancy and lactation and their possible side effects are described and discussed. Expert opinion: Mechanism of action and metabolism of these drugs as well as patients’ clinical characteristics can affect the safety of treatment. All approved medications are valid tools for the treatment of AUD in patients without advanced liver disease. For some drugs, attention should be paid to patients with renal failure and medications may be used with caution, adjusting the dosage according to kidney function. In patients with AUD and advanced liver disease, at present only baclofen has been formally tested in randomized controlled trials showing its safety in this population.
Unraveling Oligodendrocyte Origin and Function by Cell-Specific Transgenesis

Besides the role of mature oligodendrocytes in myelin synthesis during the development of the central nervous system (CNS), the oligodendrocyte lineage also encompasses the largest pool of postnatal proliferating progenitors whose behavior in vivo remains broadly elusive in health and disease. We describe here transgenic models that allow us to track the functions and origins of such cells by using proteolipid protein and 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNP) gene promoters to direct oligodendroglial expression of different reporters, in particular the green fluorescent protein (GFP). We emphasize that the CNP-GFP mouse, which targets the entire oligodendroglial lineage from embryonic life to adulthood, provides an outstanding tool to study the in vivo properties of oligodendrocyte progenitor cells in normal and damaged CNS.
Critical Role for Monocytes/Macrophages in Rapid Progression to AIDS in Pediatric Simian Immunodeficiency Virus-Infected Rhesus Macaques

ABSTRACT Infant humans and rhesus macaques infected with the human or simian immunodeficiency virus (HIV or SIV), respectively, express higher viral loads and progress more rapidly to AIDS than infected adults. Activated memory CD4+ T cells in intestinal tissues are major primary target cells for SIV/HIV infection, and massive depletion of these cells is considered a major cause of immunodeficiency. Monocytes and macrophages are important cells of innate immunity and also are targets of HIV/SIV infection. We reported previously that a high peripheral blood monocyte turnover rate was predictive for the onset of disease progression to AIDS in SIV-infected adult macaques. The purpose of this study was to determine if earlier or higher infection of monocytes/macrophages contributes to the more rapid progression to AIDS in infants. We observed that uninfected infant rhesus macaques exhibited higher physiologic baseline monocyte turnover than adults. Early after SIV infection, the monocyte turnover further increased, and it remained high during progression to AIDS. A high percentage of terminal deoxynucleotidyltransferase dUTP nick end label (TUNEL)-positive macrophages in the lymph nodes (LNs) and intestine corresponded with an increasing number of macrophages derived from circulating monocytes (bromodeoxyuridine positive [BrdU+] CD163+), suggesting that the increased blood monocyte turnover was required to rapidly replenish destroyed tissue macrophages. Immunofluorescence analysis further demonstrated that macrophages were a significant portion of the virus-producing cells found in LNs, intestinal tissues, and lungs. The higher baseline monocyte turnover in infant macaques and subsequent macrophage damage by SIV infection may help explain the basis of more rapid disease progression to AIDS in infants. IMPORTANCE HIV infection progresses much more rapidly in pediatric cases than in adults; however, the mechanism for this difference is unclear. Using the rhesus macaque model, this work was performed to address why infants infected with SIV progress more quickly to AIDS than do adults. Earlier we reported that in adult rhesus macaques, increasing monocyte turnover reflected tissue macrophage damage by SIV and was predictive of terminal disease progression to AIDS. Here we report that uninfected infant rhesus macaques exhibited a higher physiological baseline monocyte turnover rate than adults. Furthermore, once infected with SIV, infants displayed further increased monocyte turnover that may have facilitated the accelerated progression to AIDS. These results support a role for monocytes and macrophages in the pathogenesis of SIV/HIV and begin to explain why infants are more prone to rapid disease progression.
Fine structure of conformational ensembles in adenylate kinase

Adenylate kinase (ADK) catalyzes the reversible Mg2+‐dependent phosphoryl transfer reaction Mg2++2ADP ↔Mg2++ATP + AMP in essential cellular systems. This reaction is a major player in cellular energy homeostasis and the isoform network of ADK plays an important role in AMP metabolic signaling circuits. ADK has 3 domains, the LID, NMP, and CORE domains, that undergo large conformational rearrangements during ADK's catalytic cycle. In spite of extensive experimental and computational studies, details of the conformational pathway from open to closed forms remain uncertain. In this paper we explore this pathway using coarse‐grained molecular dynamics (MD) trajectories of ADK calculated by GROMACS using a SMOG model and classify the conformations within the resultant trajectories by K‐means clustering. ADK conformations segregate naturally into open; intermediate; and closed forms with long‐term residence in the intermediate state. Structural clustering divides the intermediate conformation into 3 sub‐states that are distinguished from one another on the basis of differences in both structure and dynamics. These distinctions are defined on the basis of a number of different metrics including radius of gyration, dihedral angle fluctuation, and fluctuations of interatomic pair distances. Furthermore, differences in the sub‐states appear to correspond to the distinct ways each sub‐state contributes to the molecular mechanism of catalysis: One sub‐state acts as a gate‐way to the open conformation; one sub‐state a gate‐way to the closed conformation. A third intermediate sub‐state appears to represent a metastable off‐pathway structure that is nevertheless frequently visited during the passage from open to closed state.