Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of Pol32 in Drosophila melanogaster Causes Chromosome Instability and Suppresses Variegation

Pol32 is an accessory subunit of the replicative DNA Polymerase δ and of the translesion Polymerase ζ. Pol32 is involved in DNA replication, recombination and repair. Pol32’s participation in high- and low-fidelity processes, together with the phenotypes arising from its disruption, imply multiple roles for this subunit within eukaryotic cells, not all of which have been fully elucidated. Using pol32 null mutants and two partial loss-of-function alleles pol32rd1 and pol32rds in Drosophila melanogaster, we show that Pol32 plays an essential role in promoting genome stability. Pol32 is essential to ensure DNA replication in early embryogenesis and it participates in the repair of mitotic chromosome breakage. In addition we found that pol32 mutantssuppress position effect variegation, suggesting a role for Pol32 in chromatin architecture.
Tissue Engineering for Human Urethral Reconstruction: Systematic Review of Recent Literature

Background Techniques to treat urethral stricture and hypospadias are restricted, as substitution of the unhealthy urethra with tissue from other origins (skin, bladder or buccal mucosa) has some limitations. Therefore, alternative sources of tissue for use in urethral reconstructions are considered, such as ex vivo engineered constructs. Purpose To review recent literature on tissue engineering for human urethral reconstruction. Methods A search was made in the PubMed and Embase databases restricted to the last 25 years and the English language. Results A total of 45 articles were selected describing the use of tissue engineering in urethral reconstruction. The results are discussed in four groups: autologous cell cultures, matrices/scaffolds, cell-seeded scaffolds, and clinical results of urethral reconstructions using these materials. Different progenitor cells were used, isolated from either urine or adipose tissue, but slightly better results were obtained with in vitro expansion of urothelial cells from bladder washings, tissue biopsies from the bladder (urothelium) or the oral cavity (buccal mucosa). Compared with a synthetic scaffold, a biological scaffold has the advantage of bioactive extracellular matrix proteins on its surface. When applied clinically, a non-seeded matrix only seems suited for use as an onlay graft. When a tubularized substitution is the aim, a cell-seeded construct seems more beneficial. Conclusions Considerable experience is available with tissue engineering of urethral tissue in vitro, produced with cells of different origin. Clinical and in vivo experiments show promising results.
Hardened design based on advanced orthogonal Latin code against two adjacent multiple bit upsets (MBUs) in memories

Soft errors have been a concern in memory reliability for many years. With device feature size decreasing and memories density increasing, a single event upset (SEU) in memory may generate adjacent bit upsets in a word that may cause data errors. To avoid data errors in memories, Error Correction Codes (ECCs) are used. As multiple bits affected become frequent, the Single Error Correction (SEC) codes that can correct one bit error per word are not effective against adjacent errors and more advanced ECCs are needed. Orthogonal Latin Square (OLS) codes are a type of one-step majority logic decodable (OS-MLD) codes that have been used to protect memories recently. Although OLS codes can effectively mitigate the multiple bit upsets (MBUs), the impact on the overheads increased by the correction capability improvement is not negligible. In this paper, an optimized Orthogonal Latin Square code capable of two adjacent errors correction is proposed by optimizing the structure of OLS codes parity check matrixes using the proposed block cyclic shift algorithm. The simulation results show that the proposed code not only maintains the advantage of OS-MLD codes, but also has lower overheads than the OLS code capable of double errors correction.
Genetic Control of the Leaf Angle and Leaf Orientation Value as Revealed by Ultra-High Density Maps in Three Connected Maize Populations

Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement.
No Evidence of Enemy Release in Pathogen and Microbial Communities of Common Wasps (Vespula vulgaris) in Their Native and Introduced Range

When invasive species move to new environments they typically experience population bottlenecks that limit the probability that pathogens and parasites are also moved. The invasive species may thus be released from biotic interactions that can be a major source of density-dependent mortality, referred to as enemy release. We examined for evidence of enemy release in populations of the common wasp (Vespula vulgaris), which attains high densities and represents a major threat to biodiversity in its invaded range. Mass spectrometry proteomic methods were used to compare the microbial communities in wasp populations in the native (Belgium and England) and invaded range (Argentina and New Zealand). We found no evidence of enemy release, as the number of microbial taxa was similar in both the introduced and native range. However, some evidence of distinctiveness in the microbial communities was observed between countries. The pathogens observed were similar to a variety of taxa observed in honey bees. These taxa included Nosema, Paenibacillus, and Yersina spp. Genomic methods confirmed a diversity of Nosema spp. , Actinobacteria, and the Deformed wing and Kashmir bee viruses. We also analysed published records of bacteria, viruses, nematodes and fungi from both V. vulgaris and the related invader V. germanica. Thirty-three different microorganism taxa have been associated with wasps including Kashmir bee virus and entomophagous fungi such as Aspergillus flavus. There was no evidence that the presence or absence of these microorganisms was dependent on region of wasp samples (i.e. their native or invaded range). Given the similarity of the wasp pathogen fauna to that from honey bees, the lack of enemy release in wasp populations is probably related to spill-over or spill-back from bees and other social insects. Social insects appear to form a reservoir of generalist parasites and pathogens, which makes the management of wasp and bee disease difficult.
Pollution Breaks Down the Genetic Architecture of Life History Traits in Caenorhabditis elegans

When pollution occurs in an environment, populations present suffer numerous negative and immediate effects on their life history traits. Their evolutionary potential to live in a highly stressful environment will depend on the selection pressure strengths and on the genetic structure, the trait heritability, and the genetic correlations between them. If expression of this structure changes in a stressful environment, it becomes necessary to quantify these changes to estimate the evolutionary potential of the population in this new environment. We studied the genetic structure for survival, fecundity, and early and late growth in isogenic lines of a Caenorhabditis elegans population subject to three different environments: a control environment, an environment polluted with uranium, and a high salt concentration environment. We found a heritability decrease in the polluted environments for fecundity and early growth, two traits that were the most heritable in the control environment. The genetic structure of the traits was particularly affected in the uranium polluted environment, probably due to generally low heritability in this environment. This could prevent selection from acting on traits despite the strong selection pressures exerted on them. Moreover, phenotypic traits were more strongly affected in the salt than in the uranium environment and the heritabilities were also lower in the latter environment. Consequently the decrease in heritability was not proportional to the population fitness reduction in the polluted environments. Our results suggest that pollution can alter the genetic structure of a C. elegans population, and thus modify its evolutionary potential.
Restructuring reward processing with Mindfulness‐Oriented Recovery Enhancement: novel therapeutic mechanisms to remediate hedonic dysregulation in addiction, stress, and pain

Though valuation processes are fundamental to survival of the human species, hedonic dysregulation is at the root of an array of maladies, including addiction, stress, and chronic pain, as evidenced by the allostatic shift in the relative salience of natural reward to drug reward observed among persons with severe substance use disorders. To address this crucial problem, novel interventions are needed to restore hedonic regulatory processes gone awry in persons exhibiting addictive behaviors. This article describes a theoretical rationale and empirical evidence for the effects of one such new intervention, Mindfulness‐Oriented Recovery Enhancement (MORE), on top‐down and bottom‐up mechanisms implicated in cognitive control and hedonic regulation. MORE is innovative and distinct from extant mindfulness‐based interventions in that it unites traditional mindfulness meditation with reappraisal and savoring strategies designed to reverse the downward shift in salience of natural reward relative to drug reward, representing a crucial tipping point to disrupt the progression of addiction—a mechanistic target that no other behavioral intervention has been designed to address. Though additional studies are needed, clinical and biobehavioral data from several completed and ongoing trials suggest that MORE may exert salutary effects on addictive behaviors and the neurobiological processes that underpin them.
Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.
Development of a Prototype Over-Actuated Biomimetic Prosthetic Hand

The loss of a hand can greatly affect quality of life. A prosthetic device that can mimic normal hand function is very important to physical and mental recuperation after hand amputation, but the currently available prosthetics do not fully meet the needs of the amputee community. Most prosthetic hands are not dexterous enough to grasp a variety of shaped objects, and those that are tend to be heavy, leading to discomfort while wearing the device. In order to attempt to better simulate human hand function, a dexterous hand was developed that uses an over-actuated mechanism to form grasp shape using intrinsic joint mounted motors in addition to a finger tendon to produce large flexion force for a tight grip. This novel actuation method allows the hand to use small actuators for grip shape formation, and the tendon to produce high grip strength. The hand was capable of producing fingertip flexion force suitable for most activities of daily living. In addition, it was able to produce a range of grasp shapes with natural, independent finger motion, and appearance similar to that of a human hand. The hand also had a mass distribution more similar to a natural forearm and hand compared to contemporary prosthetics due to the more proximal location of the heavier components of the system. This paper describes the design of the hand and controller, as well as the test results.
Is Objectively Measured Sitting Time Associated with Low Back Pain? A Cross-Sectional Investigation in the NOMAD study

Background Studies on the association between sitting time and low back pain (LBP) have found contrasting results. This may be due to the lack of objectively measured sitting time or because socioeconomic confounders were not considered in the analysis. Objectives To investigate the association between objectively measured sitting time (daily total, and occupational and leisure-time periods) and LBP among blue-collar workers. Methods Two-hundred-and-one blue-collar workers wore two accelerometers (GT3X+ Actigraph) for up to four consecutive working days to obtain objective measures of sitting time, estimated via Acti4 software. Workers reported their LBP intensity the past month on a scale from 0 (no pain) to 9 (worst imaginable pain) and were categorized into either low (≤5) or high (>5) LBP intensity groups. In the multivariate-adjusted binary logistic regression analysis, total sitting time, and occupational and leisure-time sitting were both modeled as continuous (hours/day) and categorical variables (i.e. low, moderate and high sitting time). Results The multivariate logistic regression analysis showed a significant positive association between total sitting time (per hour) and high LBP intensity (odds ratio; OR=1.43, 95%CI=1.15-1.77, P=0.01). Similar results were obtained for leisure-time sitting (OR=1.45, 95%CI=1.10-1.91, P=0.01), and a similar but non-significant trend was obtained for occupational sitting time (OR=1.34, 95%CI 0.99-1.82, P=0.06). In the analysis on categorized sitting time, high sitting time was positively associated with high LBP for total (OR=3.31, 95%CI=1.18-9.28, P=0.03), leisure (OR=5.31, 95%CI=1.57-17.90, P=0.01), and occupational (OR=3.26, 95%CI=0.89-11.98, P=0.08) periods, referencing those with low sitting time. Conclusion Sitting time is positively associated with LBP intensity among blue-collar workers. Future studies using a prospective design with objective measures of sitting time are recommended.
Surface-Modified Substrates for Quantum Dot Inks in Printed Electronics

Printed electronics fill the niches for low-cost, flexible devices in electronics. Developing substrates suitable for various printable electronic inks becomes an important topic in both academia and industry. Because of their extraordinary properties like solution processability, colloidal quantum dots (QDs) are gradually emerging in this field as promising candidates for electronic inks. In recent years, researchers have successfully produced high quality PbS QD inks in polar solvents. However, the incorporation of electronic inks onto a well-passivated substrate remains challenging due to the processing incompatibility between polar solvents and hydrophobic substrates. Here, we propose a surface modification strategy by using chlorine to achieve both trap-site suppression and a hydrophilic surface. The chlorine can effectively passivate the surface dangling bonds and charged hydroxyls while creating a hydrophilic surface. On this modified substrate, the contact angle between the water droplet and the SiO2 substrate can be as small as 20° and this strategy is also feasible for other polymer and inorganic substrates. For a proof-of-concept demonstration, we fabricated a PbS QD ink-based field-effect transistor on a Cl-passivated substrate, and the device showed a mobility as high as 4.36 × 10–3 cm2/V s, which indicates effective trap-site suppression. This device also enables the potential of the Cl-passivated substrates for QD inks with water or other polar solvents.
Giving the Help That Is Needed

Social support is most effective when it meets recipients’ needs. Guided by regulatory mode theory, this article examines how support providers’ chronic motivational concerns with assessment and locomotion shape help provision. We hypothesized that stronger assessment concerns motivate helpers to “tailor” support efforts by offering support that meets helpees’ specific motivational concerns and not offering support that would fail to address these concerns. In contrast, we predicted that stronger locomotion concerns motivate helpers to offer both support that fits helpees’ needs and support that does not. The results of Studies 1 and 2, using hypothetical scenarios, were consistent with these hypotheses. Study 3 replicated these findings in support interactions among friend pairs, and also found that helper assessment predicted greater support tailoring, which in turn predicted helpees’ negative mood improvement. Chronic assessment and locomotion concerns direct support efforts and influence the extent to which support is beneficial.
Ecological and Geographical Analysis of the Distribution of the Mountain Tapir (Tapirus pinchaque) in Ecuador: Importance of Protected Areas in Future Scenarios of Global Warming

In Ecuador, Tapirus pinchaque is considered to be critically endangered. Although the species has been registered in several localities, its geographic distribution remains unclear, and the effects of climate change and current land uses on this species are largely unknown. We modeled the ecological niche of T. pinchaque using MaxEnt, in order to assess its potential adaptation to present and future climate change scenarios. We evaluated the effects of habitat loss due by current land use, the ecosystem availability and importance of Ecuadorian System of Protected Areas into the models. The model of environmental suitability estimated an extent of occurrence for species of 21,729 km2 in all of Ecuador, mainly occurring along the corridor of the eastern Ecuadorian Andes. A total of 10 Andean ecosystems encompassed ~98% of the area defined by the model, with herbaceous paramo, northeastern Andean montane evergreen forest and northeastern Andes upper montane evergreen forest being the most representative. When considering the effect of habitat loss, a significant reduction in model area (~17%) occurred, and the effect of climate change represented a net reduction up to 37.86%. However, the synergistic effect of both climate change and habitat loss, given current land use practices, could represent a greater risk in the short-term, leading to a net reduction of 19.90 to 44.65% in T. pinchaque’s potential distribution. Even under such a scenarios, several Protected Areas harbor a portion (~36 to 48%) of the potential distribution defined by the models. However, the central and southern populations are highly threatened by habitat loss and climate change. Based on these results and due to the restricted home range of T. pinchaque, its preference for upland forests and paramos, and its small estimated population size in the Andes, we suggest to maintaining its current status as Critically Endangered in Ecuador.
The S-Nitrosylation Status of PCNA Localized in Cytosol Impacts the Apoptotic Pathway in a Parkinson’s Disease Paradigm

It is generally accepted that nitric oxide (NO) or its derivatives, reactive nitrogen species (RNS), are involved in the development of Parkinson’s disease (PD). Recently, emerging evidence in the study of PD has indicated that protein S-nitrosylation triggers the signaling changes in neurons. In this study, SH-SY5Y cells treated with rotenone were used as a model of neuronal death in PD. The treated cells underwent significant apoptosis, which was accompanied by an increase in intracellular NO in a rotenone dose-dependent manner. The CyDye switch approach was employed to screen for changes in S-nitrosylated (SNO) proteins in response to the rotenone treatment. Seven proteins with increased S-nitrosylation were identified in the treated SH-SY5Y cells, which included proliferating cell nuclear antigen (PCNA). Although PCNA is generally located in the nucleus and participates in DNA replication and repair, significant PCNA was identified in the SH-SY5Y cytosol. Using immunoprecipitation and pull-down approaches, PCNA was found to interact with caspase-9; using mass spectrometry, the two cysteine residues PCNA-Cys81 and -Cys162 were identified as candidate S-nitrosylated residues. In addition, the evidence obtained from in vitro and the cell model studies indicated that the S-nitrosylation of PCNA-Cys81 affected the interaction between PCNA and caspase-9. Furthermore, the interaction of PCNA and caspase-9 partially blocked caspase-9 activation, indicating that the S-nitrosylation of cytosolic PCNA may be a mediator of the apoptotic pathway.
Designing computer systems with MEMS-based storage

For decades the RAM-to-disk memory hierarchy gap has plagued computer architects. An exciting new storage technology based on microelectromechanical systems (MEMS) is poised to fill a large portion of this performance gap, significantly reduce system power consumption, and enable many new applications. This paper explores the system-level implications of integrating MEMS-based storage into the memory hierarchy. Results show that standalone MEMS-based storage reduces I/O stall times by 4--74X over disks and improves overall application runtimes by 1.9--4.4X. When used as on-board caches for disks, MEMS-based storage improves I/O response time by up to 3.5X. Further, the energy consumption of MEMS-based storage is 10--54X less than that of state-of-the-art low-power disk drives. The combination of the high-level physical characteristics of MEMS-based stor-age (small footprints, high shock tolerance) and the ability to directly integrate MEMS-based storage with processing leads to such new applications as portable gigabit storage systems and ubiquitous active storage nodes.