Miracle-dz/UniFAR-FTUs huggingface dataset:
The physiological acclimation and growth response of Populus trichocarpa to warming.

Plant metabolic acclimation to thermal stress remains underrepresented in current global climate models. Gaps exist in our understanding of how metabolic processes (i.e., photosynthesis, respiration) acclimate over time and how aboveground versus belowground acclimation differs. We measured the thermal acclimation of Populus trichocarpa, comparing aboveground vs. belowground physiology over time. Ninety genetically identical ramets were propagated in mesocosms that separated root and microbial components. After establishment at 25°C for six weeks, sixty clones were warmed +4°C or +8°C and monitored for ten weeks, measuring photosynthesis (A), leaf respiration (R), soil respiration (Rs ), root plus soil respiration (Rs+r ), and root respiration (Rr ). We observed thermal acclimation in both A and R, with rates initially increasing, then declining as the thermal photosynthetic optimum (Topt ) and the temperature-sensitivity (Q10 ) of respiration adjusted to warmer conditions. Photosynthetic acclimation was constructive, based on an increase in both Topt and peak A. Belowground, Rs+r decreased linearly with warming, while Rs rates declined abruptly, then remained constant with additional warming. Plant biomass was greatest at +4°C, with 30% allocated belowground. Rates of mass-based Rr were similar among treatments; however, root nitrogen declined at +8°C leading to less mass nitrogen-based Rr in that treatment. The Q10 -temperature relationship of Rr was affected by warming, leading to differing values among treatments. Aboveground acclimation exceeded belowground acclimation, and plant nitrogen-use mediated the acclimatory response. Results suggest that moderate climate warming (+4°C) may lead to acclimation and increased plant biomass production but increases in production could be limited with severe warming (+8°C). This article is protected by copyright. All rights reserved.
Phylogenomics of Opsin Genes in Diptera Reveals Lineage-Specific Events and Contrasting Evolutionary Dynamics in Anopheles and Drosophila

Abstract Diptera is one of the biggest insect orders and displays a large diversity of visual adaptations. Similarly to other animals, the dipteran visual process is mediated by opsin genes. Although the diversity and function of these genes are well studied in key model species, a comprehensive comparative genomic study across the dipteran phylogeny is missing. Here we mined the genomes of 61 dipteran species, reconstructed the evolutionary affinities of 528 opsin genes, and determined the selective pressure acting in different species. We found that opsins underwent several lineage-specific events, including an independent expansion of Long Wave Sensitive opsins in flies and mosquitoes, and numerous family-specific duplications and losses. Both the Drosophila and the Anopheles complement are derived in comparison with the ancestral dipteran state. Molecular evolutionary studies suggest that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher in Anopheles than in Drosophila. Overall, our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations, Anopheles and Drosophila, are characterized by contrasting dynamics in the evolution of this gene family. These results provide a foundation for future studies on the dipteran visual system.
A Submillimeter Continuous Variable Stiffness Catheter for Compliance Control

Minimally invasive robotic surgery often requires functional tools that can change their compliance to adapt to the environment and surgical needs. This paper proposes a submillimeter continuous variable stiffness catheter equipped with a phase‐change alloy that has a high stiffness variation in its different states, allowing for rapid compliance control. Variable stiffness is achieved through a variable phase boundary in the alloy due to a controlled radial temperature gradient. This catheter can be safely navigated in its soft state and rigidified to the required stiffness during operation to apply a desired force at the tip. The maximal contact force that the catheter applies to tissue can be continuously modified by a factor of 400 (≈20 mN–8 N). The catheter is equipped with a magnet and a micro‐gripper to perform a fully robotic ophthalmic minimally invasive surgery on an eye phantom by means of an electromagnetic navigation system.
One hundred years of zoonoses research in the Horn of Africa: A scoping review

Background One Health is particularly relevant to the Horn of Africa where many people’s livelihoods are highly dependent on livestock and their shared environment. In this context, zoonoses may have a dramatic impact on both human and animal health, but also on country economies. This scoping review aimed to characterise and evaluate the nature of zoonotic disease research in the Horn region. Specifically, it addressed the following questions: (i) what specific zoonotic diseases have been prioritised for research, (ii) what data have been reported (human, animal or environment), (iii) what methods have been applied, and (iv) who has been doing the research? Methodology/principal findings We used keyword combinations to search online databases for peer-reviewed papers and theses. Screening and data extraction (disease, country, domain and method) was performed using DistillerSR. A total of 2055 studies focusing on seven countries and over 60 zoonoses were included. Brucellosis attracted the highest attention in terms of research while anthrax, Q fever and leptospirosis have been comparatively under-studied. Research efforts did not always align with zoonoses priorities identified at national levels. Despite zoonoses being a clear target for ‘One Health’ research, a very limited proportion of studies report data on the three domains of human, animal and environment. Descriptive and observational epidemiological studies were dominant and only a low proportion of publications were multidisciplinary. Finally, we found that a minority of international collaborations were between Global South countries with a high proportion of authors having affiliations from outside the Horn of Africa. Conclusions/significance There is a growing interest in zoonoses research in the Horn of Africa. Recommendations arising from this scoping review include: (i) ensuring zoonoses research aligns with national and global research agendas; (ii) encouraging researchers to adopt a holistic, transdisciplinary One Health approach following high quality reporting standards (COHERE, PRISMA, etc.); and (iii) empowering local researchers supported by regional and international partnerships to engage in zoonoses research.
Biofunctionalization of bioactive ceramic scaffolds to increase the cell response for bone regeneration

Biofunctionalization was investigated for polymers and metals considering their scarce integration ability. On the contrary few studies dealt with ceramic biofunctionalization because the bioactive and bioresorbable surfaces of ceramics are able to positively interact with biological environment. In this study the cell-response improvement on biofunctionalized wollastonite and diopside-based scaffolds was demonstrated. The ceramics were first obtained by heat treatment of a silicone embedding reactive oxide fillers and then biofunctionalized with adhesive peptides mapped on vitronectin. The most promising in vitro results, in terms of h-osteoblast proliferation and bone-related gene expression, were reached anchoring selectively a peptide stable toward proteolytic degradation induced by serum-enriched medium. In in vivo assays the anchoring of this protease-stable adhesive peptide was combined with self-assembling peptides, for increasing cell viability and angiogenesis. The results demonstrated external and internal cell colonization of biofunctionalized scaffolds with formation of new blood vessels (neoangiogenesis) and stimulation of ectopic mineralization.
Impact of the use of multiplex PCR on etiological diagnosis and treatment of acute respiratory infections in a private hospital of the north of the country.

Background and objective Diseases of the respiratory system represent one of the leading causes of medical care and antibiotic prescriptions. Currently, new technologies are used for the diagnosis of respiratory diseases of viral origin, such as the FilmArray Respiratory Panel®, approved in 2012 by the FDA. The purpose of this study was to identify the correlation between the diagnosis and treatment of respiratory tract infections and the result of the polymerase chain reaction test for respiratory viruses. Material and methods The study is of a retrospective, cross-sectional, descriptive type. One-hundred and thirty-four patients who underwent a viral panel for respiratory viruses, which was positive for one or more viruses, were included. For all cases, the positive results of said test and the treatment received by patients were analyzed. Results Of the patients who underwent nasopharyngeal aspirate during hospitalization, 58 % received antibiotic treatment at admission, 13 % received combined treatment (antibiotic + antiviral), 27 % of the patients received symptomatic treatment since admission and 2 % did it with antivirals. After receiving a positive result for respiratory viruses, 38 % continued with antibiotics, 30 % with antibiotics and antivirals, 13.8 % were managed only with antivirals and 18.2 % with symptomatic treatment. Conclusion Despite the global alert regarding antimicrobial resistance, patients continue to be treated with antibiotics, due to a situation that we ignore, but that is believed to be influenced by several factors.
Framework built on resource based view for outsourcing strategy on hiring logistics service provider

Abstract The process of Outsourcing Logistics Service (OLS) is deemed incipient in the management of organizations, not only because of the operational problems it presents, but also of its difficulties fitting into the company’s overall strategy. The present theoretical study, building on the resource-based view of the firm, aims to propose a framework that guides managers in developing strategies to OLS starting from the operational structure to establish the necessary resources, capabilities, and routines. In addition, taken into account is the importance of analyzing risks and resilience in the environment, concomitantly with the analysis of the operational structure. Thus, four questions were developed, aimed at leading operations managers to reflect on the development of the strategy. The framework proposed for OLS considers the supply chain management department as the main interlocutor of the strategy. This framework can be adapted according with the necessity of the contracting company, and its main intention is to enable the establishment of a project that contemplates the necessary resources, the capabilities (criteria), and the operational routines (subcriteria) for the selection of a logistics service provider in the market, one which truly addresses the needs of the organization. This framework is already intrinsic in the practical actions of the authors, because of their extensive advisory activity over the last five years in OLS to logistics service provider. In addition, it is worth mentioning that so far in the tacit applications of this framework there has been no application similar to another.
Identifying the Key Risk Factors of Mega Infrastructure Projects from an Extended Sustainable Development Perspective

Mega infrastructure projects (MIPs) have become increasingly important to the realization of sustainable development in China. Sustainable development is a process of dynamic balance, and coordinating the triple bottom line (the environmental, social, and economic dimensions) will enable more sustainable development of MIPs. However, previous studies have lacked consideration of coordination when applying sustainable development principles to the systematic identification of risks to MIPs. The goals of this study were to clarify the definition and dimensions of the sustainable development of MIPs and to identify the key risks of MIPs. A literature review was performed to extend the definition of sustainable development of MIPs by combining the triple bottom line with a fourth coordination dimension. A conceptual model of MIP risk identification was then proposed from an extended sustainable development perspective, 22 sustainability elements and 75 risk factors were identified, and the key risk factors were determined based on the interview responses and fuzzy set theory. The results show that economic risks have a high probability, social risks have a high loss, environmental risks have an intermediate probability and loss, and coordination risks have the greatest impact. In addition, the three most important key risk factors were found to be construction and installation cost overruns, land acquisition and resettling cost overruns, and information sharing with the public. Identifying key risk factors can provide information to help stakeholders understand the risk factors associated with MIPs and formulate reasonable risk response strategies.
On Broken Triangles (IJCAI 2016)

A binary CSP instance satisfying the broken-triangle property (BTP) can be solved in polynomial time. Unfortunately, in practice, few instances satisfy the BTP. We show that a local version of the BTP allows the merging of domain values in binary CSPs, thus providing a novel polynomial-time reduction operation. Experimental trials on benchmark instances demonstrate a signiﬁcant decrease in instance size for certain classes of problems. We show that BTP-merging can be generalised to instances with constraints of arbitrary arity. A directional version of the general-arity BTP then allows us to extend the BTP tractable class previously de-ﬁned only for binary CSP.
Coupled mode analysis of high-speed transverse coupled cavity vertical-cavity surface-emitting laser for low frequency chirp operations

We demonstrate the modeling and experimental results on the modulation bandwidth and frequency chirp of the transverse coupled cavity vertical-cavity surface-emitting lasers (TCC-VCSELs). Both a 3-dB- modulation bandwidth enhancement and chirp reduction are shown in the results. These improvements could be explained by an increase in differential net gain and photon-photon resonance introduced by strong coupling in coupled cavities. Our TCC VCSEL could be useful for higher data rates and longer link lengths of single-mode fiber transmissions.
Effect of Grape Over-Ripening and Its Skin Presence on White Wine Alcoholic Fermentation in a Warm Climate Zone

The current trend of rising temperatures and sun irradiation associated to climate change is pushing traditional grape-producing areas with a warm climate towards a very accelerated ripening, leading to earlier harvesting dates and grape must with an unbalanced composition. However, this climatic trend could be exploited to produce other types of wine. In this sense, the increase in temperature could be used to produce wines with overripe grapes. In this regard, the aim of this research work is to evaluate the influence of different degrees and techniques of grape over-ripening to produce wines with the presence or absence of its skins during alcoholic fermentation. To this end, a physicochemical characterization of grape musts and wines obtained from overripe grapes and the monitoring of their fermentation has been performed. Over-ripening grapes by sun-drying has been established as a viable technique viability, producing musts and wines with unique physicochemical and sensory characteristics. In view of the above, it is considered that the production of wines from overripe grapes and in the presence or absence of grape skins is a viable approach to make new white wines taking advantage of the conditions imposed by climate change in a warm climate zone and meet the trends and expectations of current wine consumers.
Periodic Surge Origin of Folded Medial Moraines on Bering Piedmont Glacier, Alaska

Abstract The vast Bering piedmont glacier, which has large folds in the medial moraines in its terminal lobe, recently experienced two surges with a combined ice displacement of as much as 13 km. Vertical aerial photographs taken before and after the surges disclose the direction and magnitude of ice flow in various parts of the piedmont lobe. The ice moved toward the terminus and expanded in a normal, radial pattern with no evidence of unusual shearing that would result in the formation of large folds. Many surging glaciers display repeated lateral displacements in their medial moraines which result from periodic surging of the main glacier past non-surging tributaries. Moraines of Bering Glacier display small periodic irregularities of this nature. The large “accordion” folds in the moraines in the piedmont lobe are judged to be due to the combined effects of compressive flow and lateral or transverse expansion of these previously formed irregularities. The initially small pre-existing perturbations in the moraines are simply spread laterally and shortened radially into large folds as the ice spreads out. A very large debris band composed of repeatedly folded medial moraines extends across the center of the Bering Glacier lobe. These remarkable folds are thought to result from the deformation of surge-related irregularities in medial moraines as they pass through the zone of intensive shear near the glacier’s margin.
Social Media Conversations About High Engagement Sports Team Brands

This study conducts an analysis of social media discussions related to high engagement sports brands. More specifically, our study examined the English Premier League (EPL); it sought to retrieve data systematically over the same day, weekly, for a period of five months. After this process, we had built 20 datasets and NodeXL was utilized to analyse the data. After we had this data, we were able to use qualitative observations to identify key users and conversations that formed around the EPL as well as the connections between the conversations that arose from the brand’s posts and the people involved in them. We also analyzed the quantitative data underpinning our network visualisations to provide further insights. The most obvious initial finding was that when the EPL tweets, it prompts a large volume of conversations directly related to these tweets. However, we also noted that EPL tweets also help instigate further, sometimes unrelated, tweets and conversations. More specifically, we identified that the visualized network of conversations was of a broadcast form, which is characterized by messages being generated by a central account (the EPL) and shared by a number of decentralized users. Based on our analysis, we propose guidance around (S)ocial media presence, (C)rafting the message, Planned (i)ntervention, (S)pontaneous follow-up, and (M)essage mortality to form the SCISM framework. This framework is likely to be of interest to brands that wish to promote, sustain and benefit from their instigation of social media.
Securing CHEESEHub: A Cloud-based, Containerized Cybersecurity Education Platform

The Cyber Human Ecosystem for Engaged Security Education (CHEESEHub) is an open web platform that hosts community-contributed containerized demonstrations of cybersecurity concepts. In order to maximize flexibility, scalability, and utilization, CHEESEHub is currently hosted in a Kubernetes cluster on the Jetstream academic cloud. In this short paper, we describe the security model of CHEESEHub and specifically the various Kubernetes security features that have been leveraged to secure CHEESEHub. This ensures that the various cybersecurity exploits hosted in the containers cannot be misused, and that potential malicious users of the platform are cordoned off from impacting not just other legitimate users, but also the underlying hosting cloud. More generally, we hope that this article will provide useful information to the research computing community on a less discussed aspect of cloud deployment: the various security features of Kubernetes and their application in practice.
Revisiting integration in the material point method

The material point method (MPM) recently demonstrated its efficacy at simulating many materials and the coupling between them on a massive scale. However, in scenarios containing debris, MPM manifests more dissipation and numerical viscosity than traditional Lagrangian methods. We have two observations from carefully revisiting existing integration methods used in MPM. First, nearby particles would end up with smoothed velocities without recovering momentum for each particle during the particle-grid-particle transfers. Second, most existing integrators assume continuity in the entire domain and advect particles by directly interpolating the positions from deformed nodal positions, which would trap the particles and make them harder to separate. We propose an integration scheme that corrects particle positions at each time step. We demonstrate our method's effectiveness with several large-scale simulations involving brittle materials. Our approach effectively reduces diffusion and unphysical viscosity compared to traditional integrators.
Learning contact corrections for handle-based subspace dynamics

This paper introduces a novel subspace method for the simulation of dynamic deformations. The method augments existing linear handle-based subspace formulations with nonlinear learning-based corrections parameterized by the same subspace. Together, they produce a compact nonlinear model that combines the fast dynamics and overall contact-based interaction of subspace methods, with the highly detailed deformations of learning-based methods. We propose a formulation of the model with nonlinear corrections applied on the local undeformed setting, and decoupling internal and external contact-driven corrections. We define a simple mapping of these corrections to the global setting, an efficient implementation for dynamic simulation, and a training pipeline to generate examples that efficiently cover the interaction space. Altogether, the method achieves unprecedented combination of speed and contact-driven deformation detail.
Markets, Tort Law, and Regulation to Achieve Safety

Markets, tort law, and direct regulation are alternative methods of achieving safety. Of these, the market is the most powerful, but it is often ignored in policy discussions. I show that both for the U.S. over time and for the world as a whole, higher incomes are associated with lower death rates, and I discuss some examples of markets creating safety. Markets may fail if there are third party effects or if there are information problems. Classic tort law is a reasonable (although expensive) way to handle third party effects for strangers, as in the case of auto accidents. In theory, regulation could solve information problems, but in practice many regulations overreach because of different information problems – consumers are unaware of unapproved alternatives. A particularly difficult information problem arises in the case of what I call “ambiguous” goods – goods that reduce some risks but increase others (as medical care and malpractice.) Product liability focuses on these goods; over half of the "litigation groups" of the American Association for Justice are for ambiguous goods. Increasing the price of these goods through tort liability may make consumers worse off because they are less likely to purchase more expensive goods. At least in the case of drugs both the regulatory system and the tort system are probably overly restrictive so using both is likely to lead to net consumer harm. This would argue for preemption – FDA approval should preempt state tort law.