Miracle-dz/UniFAR-FTUs huggingface dataset:
Drought activates MYB41 orthologs and induces suberization of grapevine fine roots

Abstract The permeability of roots to water and nutrients is controlled through a variety of mechanisms and one of the most conspicuous is the presence of the Casparian strips and suberin lamellae. Roots actively regulate the creation of these structures developmentally, along the length of the root, and in response to the environment, including drought. In the current study, we characterized the suberin composition along the length of grapevine fine roots during development and in response to water deficit, and in the same root systems we quantified changes in expression of suberin biosynthesis‐ and deposition‐related gene families (via RNAseq) allowing the identification of drought‐responsive suberin‐related genes. Grapevine suberin composition did not differ between primary and lateral roots, and was similar to that of other species. Under water deficit there was a global upregulation of suberin biosynthesis which resulted in an increase of suberin specific monomers, but without changes in their relative abundances, and this upregulation took place across all the developmental stages of fine roots. These changes corresponded to the upregulation of numerous suberin biosynthesis‐ and export‐related genes which included orthologs of the previously characterized AtMYB41 transcriptional factor. Functional validation of two grapevine MYB41 orthologs, VriMYB41 and VriMYB41‐like, confirmed their ability to globally upregulate suberin biosynthesis, export, and deposition. This study provides a detailed characterization of the developmental and water deficit induced suberization of grapevine fine roots and identifies important orthologs responsible for suberin biosynthesis, export, and its regulation in grape.
Overexpression of miRNA-145 induces apoptosis and prevents proliferation and migration of MKN-45 gastric cancer cells

MiR-145 is a tumor suppressor miRNA that its ubiquitously expressed in the body but in numerous types of cancers such as GC, its expression became reduced or sometimes ceased in many subjects. This study aimed at restoring the function of the miR-145 in MKN-45 cells and investigating the function of this miRNA in proliferation, apoptosis, and migration of GC cells. MKN-45 cells were transfected using the PCMV-miR-145 plasmid vector. The MTT, DAPI staining, and wound healing assays were applied to estimate the impacts of ectopic expression of miR-145 in vitro. Moreover, alterations in the expression levels of K-Ras, c-Myc, caspase-3, caspase-9, Bax, Bcl-2, and MMP-9 mRNA were measured by qRT-PCR analysis. The findings designated that high expression of miR-145 reduced the proliferation and migration and increased the apoptosis of the MKN-45 cells. These effects occur with concurrent suppression of c-Myc, K-Ras, Bcl-2, and MMP-9 as well as induction of caspase-3, caspase-9, and Bax expression. Exogenous miR-145 influences multiple oncogenic pathways and can be regarded as a promising avenue of future therapeutic interventions for GC therapy.
Impact of an Extracorporeal Membrane Oxygenation Intensivist-Led Multidisciplinary Team on Venovenous Extracorporeal Membrane Oxygenation Outcomes

Objectives: Venovenous extracorporeal membrane oxygenation is increasingly being established as a treatment option for severe acute respiratory failure. We sought to evaluate the impact of a dedicated specialist team-based approach on patient outcomes. Design: Retrospective cohort study. Setting: Single-center medical ICU in an academic tertiary hospital. Patients: Adult patients initiated on venovenous extracorporeal membrane oxygenation for severe acute respiratory failure. Interventions: Initiation of an extracorporeal membrane oxygenation intensivist-led multidisciplinary team; critical decisions on extracorporeal membrane oxygenation management were jointly made by a dedicated team of extracorporeal membrane oxygenation intensivists, together with the multidisciplinary team. Measurements and Main Results: Eighty-one patients (75%) and 27 patients (35%) were initiated on venovenous extracorporeal membrane oxygenation in the preextracorporeal membrane oxygenation intensivist-led multidisciplinary team (before January 2018) and postextracorporeal membrane oxygenation intensivist-led multidisciplinary team period (after January 2018), respectively. Inhospital (14.8% vs 44.4%, p = 0.006) and ICU mortality (11.1% vs 40.7%, p = 0.005) were significantly lower in the postextracorporeal membrane oxygenation intensivist-led multidisciplinary team period. On multivariate analysis correcting for possible confounding factors (ICU severity and extracorporeal membrane oxygenation-specific mortality prediction scores, body mass index, preextracorporeal membrane oxygenation vasopressor support, preextracorporeal membrane oxygenation cardiac arrest, and days on mechanical ventilation before extracorporeal membrane oxygenation initiation), management by an extracorporeal membrane oxygenation intensivist-led multidisciplinary team remained associated with improved hospital survival (odds ratio, 5.06; 95% CI, 1.20–21.28). Patients in the postextracorporeal membrane oxygenation intensivist-led multidisciplinary team period had less nosocomial infections (18.5% vs 46.9%, p = 0.009), a shorter ICU stay (12 days [interquartile range, 6–16 d] vs 15 days [interquartile range, 10–24 d]; p = 0.049), and none suffered an intracranial hemorrhage or nonhemorrhagic stroke. Conclusions: An extracorporeal membrane oxygenation intensivist-led multidisciplinary team approach is associated with improved outcomes in patients initiated on venovenous extracorporeal membrane oxygenation for severe acute respiratory failure.
Co-Design Process of a Virtual Community of Practice for the Empowerment of People with Ischemic Heart Disease

Introduction: Virtual Communities of Practices (vCoP) offer patients the possibility to interact and share tools and knowledge necessary for their empowerment. This paper describes the co-design process of a vCoP for the empowerment of people with ischemic heart disease (IHD). Methods: We used a modified experience-based design approach to co-design the vCoP in collaboration with people with IHD and health professionals consisting of two phases: exploratory and development phase. Data collection techniques included listening labs, workshops, and online participation. Results: Twenty-five people with IHD and ten health professionals participated. Experiences and needs for empowerment in IHD were identified in the exploratory phase allowing for the development of a Patient Journey Map. In the development phase, people with IHD prioritized needs to be addressed by the vCoP content framework in addition to content proposals. Discussion: The Patient Journey Map helped to easily visualize the empowerment needs of people with IHD and it might be transferable for the development of other people-centred interventions. The co-design process also allowed the development of training materials adapted to the priorities of people with IHD. Conclusion: A people-centred co-design process of a vCoP may facilitate the empowerment of people with IHD.
Acute exacerbation in chronic bird fancier's lung with pleuroparenchymal fibroelastosis

A 71‐year‐old non‐smoker woman was admitted to our hospital complaining of a six‐month history of dry cough. She had kept java sparrow for nine years and has been raising budgerigars for the previous eight months. High‐resolution computed tomography (HRCT) images of the chest revealed reticulonodular lesions predominantly in the bilateral upper lobes. Surgical lung biopsy specimens showed non‐caseous epithelioid cell granulomas in the alveolar spaces, including irregular and centrilobular fibrosis with pleuroparenchymal fibroelastosis. When she started using a duck feather duvet at home, she developed dyspnoea and chest HRCT abnormalities progressively deteriorated. The results of precipitation of antibodies against duck feather, java sparrow, and budgerigars dropping extracts were positive in sera. Consequently, the patient was diagnosed as having chronic bird fancier's lung with acute exacerbation caused by the use of a feather duvet. After combination treatments with corticosteroid and cyclosporine, her respiratory symptoms and reticulonodular shadow immediately improved.
Giant micelles : properties and applications

Molecular Thermodynamics of Giant Micelles, R. Nagarajan Molecular Packing in Cylindrical Micelles, S. May and A. Ben-Shaul Computer Simulations of Wormlike Micelles, J. T. Padding, W.K. den Otter, and W. J. Briels Theoretical Rheology of Giant Micelles, M. Cates and S. Fielding Seeing Giant Micelles by Cryogenic-Temperature Transmission Electron Microscopy (Cryo-TEM), Y. Talmon Scattering from Wormlike Micelles, J. Skov Pedersen, L. Cannavacciouolo, and P. Schurtenberger Phase Behavior of Systems with Wormlike Micelles, F. Nettesheim and E. W. Kaler Linear Rheology of Aqueous Solutions of Wormlike Micelles, M. In Nonlinear Rheology of Giant Micelles, J.E. Puig, F. Bautista, J.F. A. Soltero, and O. Manero Relaxation in Wormlike Micelle Solutions, G. Waton and R. Zana Giant Micelles at and Near Surfaces, R. Atkin, A. Blom, and G.G. Warr Stimuli-Responsive Giant Micellar Systems, F.P. Hubbard, Jr., and N.L. Abbott Hydrogen Bonded Supramolecular Polymers versus Wormlike Micelles: Similarities and Specificities, L. Bouteiller Nonionic Block Copolymer Wormlike Micelles, Y.Y. Won and F.S. Bates Oilfield Applications of Giant Micelles, P. Sullivan, E.B. Nelson, V Anderson, and T. Hughes Drag Reduction by Surfactant Giant Micelles, J.L. Zakin, Y. Zhang, and W. Ge Giant Micelles and Shampoos, L. Nicolas-Morgantini Daily Applications of Systems with Wormlike Micelles, S. Ezrahi, E. Tuval, A. Aserin, and N. Garti
Liquids, Solutions, and Interfaces: From Classical Macroscopic Descriptions to Modern Microscopic Details

Fifty years ago solution chemistry occupied a major fraction of physical chemistry textbooks, and dealt mainly with classical thermodynamics, phase equilibria, and non-equilibrium phenomena, especially those related to electrochemistry. Much has happened in the intervening period, with tremendous advances in theory and the development of important new experimental techniques. This book brings the reader through the developments from classical macroscopic descriptions to more modern microscopic details.
Germline genomic patterns are associated with cancer risk, oncogenic pathways, and clinical outcomes

Germline variants when organized as genomic patterns are associated with cancer risk, oncogenic pathways, and clinical outcomes. There is an ongoing debate on the importance of genetic factors in cancer development, where gene-centered cancer predisposition seems to show that only 5 to 10% of the cancer cases are inheritable. By conducting a systematic analysis of germline genomes of 9712 cancer patients representing 22 common cancer types along with 16,670 noncancer individuals, we identified seven cancer-associated germline genomic patterns (CGGPs), which summarized trinucleotide mutational spectra of germline genomes. A few CGGPs were consistently enriched in the germline genomes of patients whose tumors had smoking signatures or correlated with oncogenesis- and genome instability–related mutations. Furthermore, subgroups defined by the CGGPs were significantly associated with distinct oncogenic pathways, tumor histological subtypes, and prognosis in 13 common cancer types, suggesting that germline genomic patterns enable to inform treatment and clinical outcomes. These results provided evidence that cancer risk and clinical outcomes could be encoded in germline genomes.
Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

Genomes of 150 coral colonies reveal evolutionary processes related to past climatic change on the Great Barrier Reef. Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species’ responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.
Tarantulas (Araneae: Theraphosidae) in the Pet Trade in South Africa

Many alien species have been introduced around the world as part of the pet trade, and some have escaped captivity and become invasive. In South Africa, many species of tarantula (Theraphosidae) are kept as pets. It is not known which species are traded, which are most popular, and whether their names are correctly applied. Online traders and physical pet stores were investigated between 2015 and 2016 to determine the extent or size of trade, species composition, most popular species, and their invasion history elsewhere. In total, 36 specimens, three individuals from 12 putative species, were also purchased for DNA barcoding targeting the COI gene region to quantify the accuracy of tarantula identification by traders. In total, 195 tarantula species were advertised for sale, and the most popular species were Brachypelma albopilosum Valerio, 1980 (n = 199), B. vagans Ausserer, 1875 (n = 132), and Grammostola rosea Walckenaer, 1837 (n = 120). The composition of shared species differed between the sources and most of the species were advertised online. Only one of the popular species, B. vagans, has been recorded as being invasive elsewhere. Only 36% of the barcoded specimens matched existing barcodes in online repositories that had the same species name. The three individuals from 12 putative species were not in the same terminal clade as those of conspecifics in the Barcode of Life Data System (BOLD) and the NCBI GenBank reference sequences. A large proportion of the known tarantula species are traded in South Africa and must be included in management and risk assessments to avoid potential invasions.
Trust in Colombia’s Justicia Especial Para La Paz: Experimental Evidence

Research on the determinants of institutional trust in courts that are part of transitional justice frameworks is scarce. This article relies on experimental evidence to explore whether features of the case and the ruling play a role in citizens’ attitudes towards the Justicia Especial para la Paz, Colombia’s transitional justice tribunal. I evaluate whether the profile of the accused and whether or not he is sentenced to the most lenient of restorative justice measures have an effect on trust. I find that support for the decision is lower for restorative sentences than for more punitive sentences, and that whether or not the acussed was a former guerrilla combatant or a member of the military does not influence evaluations. This research contributes to our understanding of how citizens in countries dealing with the aftermath of violence perceive the institutions devised to adjudicate on the atrocities of conflict.
The troubling trend of academic makerspaces

Abstract Technology-centered makerspaces are increasingly being built in academic libraries, typically featuring high tech machines and software that facilitate creation and design. In this essay, Juliana Mestre offers a critique such spaces highlighting several potential downsides including cost, the threat to library autonomy, and an adherence to design epistemology that overvalues the monetization of knowledge products. The essay encourages academic librarians to engage thoughtfully on the possible ramifications of makerspaces.
Adding Another Piece to the Southern African Cercopithecus Monkey Phylogeography Puzzle

The taxonomy and number of Cercopithecus monkey radiation events in southern Africa are still debated. To date, genetic studies have largely been limited to single specimens per taxon and a scattered geographical distribution. A recent study focusing on South African Cercopithecus monkeys showed that populations can be divided into three distinct genetic entities. Our current study aims to add new mtDNA and microsatellite data from a coastal population (Vamizi Island) in Mozambique to compare to existing data from South Africa. Our additional data allowed analysis of the number and timing of radiation events of Cercopithecus monkeys in southern Africa. Here we propose the occurrence of a single, north-south radiation event during the mid-Pleistocene along the Afromontane forest belt and that after the Last Glacial Maximum, samango populations reradiated into (re)established coastal forests on a more local scale. Our population genetic data support this pattern for both Mozambican, as well as South African samango monkey populations. By including mtDNA sequence data from Cercopithecus across Africa, we also discuss the hypothesis that the ‘Kingdon Line’ may explain the divergence of two major species in Africa within the C. mitis/nictitans group: C. albogularis and C. mitis.
Shape approximation by developable wrapping

We present an automatic tool to approximate curved geometries with piece-wise developable surfaces. At the center of our work is an algorithm that wraps a given 3D input surface with multiple developable patches, each modeled as a discrete orthogonal geodesic net. Our algorithm features a global optimization routine for effectively finding the placement of the developable patches. After wrapping the mesh, we use these patches and a non-linear projection step to generate a surface that approximates the original input, but is also amendable to simple and efficient fabrication techniques thanks to being piecewise developable. Our algorithm allows users to steer the trade-off between approximation power and the number of developable patches used. We demonstrate the effectiveness of our approach on a range of 3D shapes. Compared to previous approaches, our results exhibit a smaller or comparable error with fewer patches to fabricate.
A Partitioning GPU-based Algorithm for Processing the k Nearest-Neighbor Query

The k Nearest-Neighbor (k-NN) query is a common spatial query that appears in several big data applications. Typically, GPU devices have much larger numbers of processing cores than CPUs and faster device memory than main memory accessed by CPUs, thus, providing higher computing power. We propose and implement a new GPU-based partitioning algorithm for the k-NN query, using the CUDA runtime API. Due to partitioning, this algorithm avoids calculating distances for the whole dataset. Using synthetic and real datasets, we present an extensive experimental performance comparison against six existing algorithms. These algorithms are based on calculating distances for the whole in-memory dataset. This comparison shows that the new algorithm excels in all the conducted experiments and outperforms these six algorithms.
A paradoxical increase of force development in saphenous and tail arteries from heterozygous ANO1 knockout mice

A Ca2+‐activated Cl− channel protein, ANO1, is expressed in vascular smooth muscle cells where Cl− current is thought to potentiate contraction by contributing to membrane depolarization. However, there is an inconsistency between previous knockout and knockdown studies on ANO1’s role in small arteries. In this study, we assessed cardiovascular function of heterozygous mice with global deletion of exon 7 in the ANO1 gene. We found decreased expression of ANO1 in aorta, saphenous and tail arteries from heterozygous ANO1 knockout mice in comparison with wild type. Accordingly, ANO1 knockdown reduced the Ca2+‐activated Cl− current in smooth muscle cells. Consistent with conventional hypothesis, the contractility of aorta from ANO1 heterozygous mice was reduced. Surprisingly, we found an enhanced contractility of tail and saphenous arteries from ANO1 heterozygous mice when stimulated with noradrenaline, vasopressin, and K+‐induced depolarization. This difference was endothelium‐independent. The increased contractility of ANO1 downregulated small arteries was due to increased Ca2+ influx. The expression of L‐type Ca2+ channels was not affected but expression of the plasma membrane Ca2+ ATPase 1 and the Piezo1 channel was increased. Expressional analysis of tail arteries further suggested changes of ANO1 knockdown smooth muscle cells toward a pro‐contractile phenotype. We did not find any difference between genotypes in blood pressure, heart rate, pressor response, and vasorelaxation in vivo. Our findings in tail and saphenous arteries contrast with the conventional hypothesis and suggest additional roles for ANO1 as a multifunctional protein in the vascular wall that regulates Ca2+ homeostasis and smooth muscle cell phenotype.
Physiologic Target, Molecular Evolution, and Pathogenic Functions of a Monoclonal Anti–Citrullinated Protein Antibody Obtained From a Patient With Rheumatoid Arthritis

In plasma from a patient with rheumatoid arthritis (RA), we previously isolated a human monoclonal anti–citrullinated protein antibody (ACPA), CCP‐Ab1, that recognizes various citrullinated antigens. In this study, we aimed to explore the physiologic target of CCP‐Ab1 and the role of molecular evolution, through affinity maturation, of this ACPA in the onset and the exacerbation of RA.
Finite Sample System Identiﬁcation: Improved Rates and the Role of Regularization

This paper studies low-order linear system identiﬁcation via regularized regression. The nuclear norm of the system’s Hankel matrix is added as a regularizer to the least-squares cost function due to the following advantages. The regularized problem is (1) often easier to tune, (2) has lower sample complexity, and (3) returns a Hankel matrix with a clear singular value gap, which robustly recovers a low-order linear system from noisy output observations. Recently, the performance of the unregularized least-squares formulations have been studied statistically in terms of ﬁnite sample complexity and recovery errors; however, no results are known for the regularized approach. In this work, we provide a novel statistical analysis of the regularized algorithm. Our analysis leads to new bounds on estimating the impulse response and the Hankel matrix associated with the system while using smaller number of observations than the least-squares estimator.