Miracle-dz/UniFAR-FTUs huggingface dataset:
Parent-Offspring Conflict and Coadaptation

Speak to Me, Mama Maternal effects are effects of the mother (for example, hormones) on her offspring that are independent of genetic inheritance, but related to the mother's phenotype and her environment. Despite their universal occurrence, little is known about the evolutionary influence of maternal effects. Hinde et al. (p. 1373; see the cover) modeled maternal effects in birds and showed that nestling begging, as well as provoking feeding, also provides parents with information about offspring vigor. Conversely, maternal effects provide information to the unborn offspring about parental quality. Experimental studies with canaries provided support for the theoretical predictions, and together these studies show that parent-offspring conflict (that is, the conflict between the offspring for its immediate needs and the need of the parent to conserve resources for any future offspring) is resolved by the reciprocal exchange of information before and after birth. Hormonal signaling ensures a match between parental capacity for resource provisioning and offspring behavior and development after hatching that meet the mother's capacity to provide resources. Prenatal hormonal signaling can match a mother bird’s capacity to provide food with her offsprings’ expectations. The evolution of family life has traditionally been studied in parallel by behavioral ecologists and quantitative geneticists. The former focus on parent-offspring conflict and whether parents or offspring control provisioning, whereas the latter concentrate on the coadaptation of parental supply and offspring demand. Here we show how prenatal effects on offspring begging can link the two different approaches. Using theoretical and experimental analyses, we show that when offspring control provisioning, prenatal effects primarily serve the parent’s interests: Selection on parents drives coadaptation of parent and offspring traits. In contrast, when parents control provisioning, prenatal effects primarily serve the offspring’s interests: Selection on the offspring drives coadaptation of parent and offspring traits. Parent-offspring conflict may thus be responsible for the selective forces that generate parent-offspring coadaptation.
All-Inside Meniscal Repair with Bioabsorbable Meniscal Screws or with Bioabsorbable Meniscus Arrows

Background All-inside meniscal repairs have gained popularity in the past few years. However, only a few prospective, randomized clinical studies have been done to compare different all-inside meniscal repair techniques. Hypothesis Meniscal repair with bioabsorbable meniscal screws and arrows results in similar clinical outcome on short-term follow-up. Study Design Randomized controlled trial; Level of evidence, 2. Methods Forty-two patients were prospectively randomized to have all-inside meniscal repair either by using bioabsorbable meniscal screws or bioabsorbable meniscus arrows (21 patients, 23 meniscal repairs in each group) for the fixation. The evaluation methods were clinical examination, Lysholm score, the International Knee Documentation Committee (IKDC) knee score, and magnetic resonance arthrography (MRA) evaluation. The average follow-up time was 27 months (standard deviation, 8). Results There were no differences between the study groups preoperatively. All 42 patients (100%) were available for the follow-up. However, during the follow-up, 11 patients had clinical failure, confirmed at second-look arthroscopy, of the repair leading to partial meniscal resection. Four failures (all on the medial meniscus) were observed with the use of meniscal screw fixation (17%), and 7 (4 on the medial meniscus, and 3 on the lateral meniscus) with the use of meniscus arrow fixation (30%) (P = .242). Six patients with meniscus arrows (29%) had chondral damage on the femoral condyles evaluated by MRA or at second-look arthroscopy, while none of the patients with the meniscal screws had the same (P = .018). However, the Lysholm and the IKDC scores were similar in both groups at follow-up. Conclusion All-inside meniscal repair with bioabsorbable meniscal screws and arrows resulted in similar clinical outcome, although significantly more chondral damage was observed when using bioabsorbable meniscus arrows for fixation.
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

Epigenetic Maps Methylation of genomic DNA on cytosine bases provides critical epigenetic regulation of gene expression and is involved in silencing transposable elements (TEs) and repeated sequences, as well as regulating imprinted gene expression. Zemach et al. (p. 916, published online 15 April; see the Perspective by Jeltsch) analyzed DNA methylation in the genomes of five plants, five fungi, and seven animals by bisulfite sequencing. The data suggest that land plants and vertebrates, which have extensive DNA methylation, are under strong selective pressure to repress TEs, because of their sexual mode of reproduction. Unicellular animals and fungi that reproduce asexually are more likely to lose TE methylation. Although gene body methylation is evolutionarily ancient, it is also mutagenic, and so loss of this pathway has been relatively common and occurred early in fungal evolution and later in several plant and animal lineages. Analysis of DNA methylation in 17 species suggests a path for the evolution of this epigenetic mark. Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.
Carbon Dioxide Enrichment Inhibits Nitrate Assimilation in Wheat and Arabidopsis

Nitrate for Me, Ammonium for You The interdependence of plant nitrogen uptake and plant responses to carbon dioxide is well established, but the influence of inorganic nitrogen form—i.e., whether nitrate or ammonium—has been largely ignored. Bloom et al. (p. 899) present evidence from five independent methods in both a monocot and dicot species that carbon dioxide inhibition of nitrate assimilation is a major determinant of plant responses to rising atmospheric concentrations of carbon dioxide. This finding explains several phenomena, including carbon dioxide acclimation and decline in food quality. The large variation in these phenomena among species, locations, or years derives from the large variation in the relative dependence of plants on nitrate and ammonium as nitrogen sources among species, locations, or years. The relative importance of ammonium and nitrate for plant N nutrition in future cropping systems will be critical for quantity and quality of food. The inhibition of photorespiration by elevated carbon dioxide is paralleled by a reduction in the assimilation of nitrate. The concentration of carbon dioxide in Earth’s atmosphere may double by the end of the 21st century. The response of higher plants to a carbon dioxide doubling often includes a decline in their nitrogen status, but the reasons for this decline have been uncertain. We used five independent methods with wheat and Arabidopsis to show that atmospheric carbon dioxide enrichment inhibited the assimilation of nitrate into organic nitrogen compounds. This inhibition may be largely responsible for carbon dioxide acclimation, the decrease in photosynthesis and growth of plants conducting C3 carbon fixation after long exposures (days to years) to carbon dioxide enrichment. These results suggest that the relative availability of soil ammonium and nitrate to most plants will become increasingly important in determining their productivity as well as their quality as food.
Shared Social Responsibility: A Field Experiment in Pay-What-You-Want Pricing and Charitable Giving

The Greater Good Zero-sum games (if I win, then you lose) offer an easily grasped heuristic for all sorts of social interactions, especially those that involve money. For instance, companies may offer to contribute some portion of their revenues to charitable causes as an inducement to customers, but it is generally assumed that these pass-throughs directly diminish the corporate bottom line. Gneezy et al. (p. 325; see the Perspective by DellaVigna) have designed a framework that encourages both customers and companies to contribute toward social goods, and, in field tests, this design increased charitable contributions as well as corporate revenues. Exchanging goods for money ends up benefiting buyers, sellers, and charities. A field experiment (N = 113,047 participants) manipulated two factors in the sale of souvenir photos. First, some customers saw a traditional fixed price, whereas others could pay what they wanted (including $0). Second, approximately half of the customers saw a variation in which half of the revenue went to charity. At a standard fixed price, the charitable component only slightly increased demand, as similar studies have also found. However, when participants could pay what they wanted, the same charitable component created a treatment that was substantially more profitable. Switching from corporate social responsibility to what we term shared social responsibility works in part because customized contributions allow customers to directly express social welfare concerns through the purchasing of material goods.
Foot Orthoses in the Prevention of Injury in Initial Military Training

Background: Overuse lower limb injury is common in incidence and morbidity. Many risk factors, gait related and biomechanical, have been identified, although little conclusive evidence has been found in terms of injury prevention to date. Hypothesis: Orthoses, as produced by proprietary software interpretation of plantar pressures, are able to reduce injury rates in an “at risk” military population. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: Four hundred military officer trainees were assessed by means of pressure plate recording of their contact foot pressures during walking. Participants were risk assessed and randomized to receive or not receive customized orthoses using the D3D system. Both cohorts were followed up for injury through their basic training at the 7-week point. Results: The orthotic intervention group sustained 21 injuries in total (1 injury per 4666 hours of training), whereas the control group sustained 61 injuries in total (1 injury per 1600 hours of training) (P < .0001), thereby demonstrating an absolute risk reduction of 0.49 from use of the orthoses (P < .0001, chi square; confidence interval, 1.7, 2.4). Conclusion: In this military trainee population, orthoses were effective in the prevention of overuse lower limb injury. This is the first study to identify a positive preventive role of orthoses.
Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

Everything Changes Nucleosomes package DNA, and their assembly and disassembly regulate access to the genome. The ability to follow these changes is limited to steady-state methods in higher eukaryotes, although direct kinetic analyses are available in yeast. To address this deficiency, Deal et al. (p. 1161) developed a general method for following the genome-wide dynamics of nucleosome assembly and disassembly. High levels of nucleosome turnover were observed across gene bodies and at the sites of epigenetic regulatory elements in fruit fly tissue culture cells. Nucleosomes were replaced multiple times during each 20-hour cell cycle, suggesting that histone modifications themselves are unlikely to transmit epigenetic information. Furthermore, analysis of replication origins indicates that they are determined by chromatin dynamics and not by sequence features. Differences between active and silent chromatin states are critical for maintaining the epigenome. Nucleosome disruption and replacement are crucial activities that maintain epigenomes, but these highly dynamic processes have been difficult to study. Here, we describe a direct method for measuring nucleosome turnover dynamics genome-wide. We found that nucleosome turnover is most rapid over active gene bodies, epigenetic regulatory elements, and replication origins in Drosophila cells. Nucleosomes turn over faster at sites for trithorax-group than polycomb-group protein binding, suggesting that nucleosome turnover differences underlie their opposing activities and challenging models for epigenetic inheritance that rely on stability of histone marks. Our results establish a general strategy for studying nucleosome dynamics and uncover nucleosome turnover differences across the genome that are likely to have functional importance for epigenome maintenance, gene regulation, and control of DNA replication.
Fairness and the Development of Inequality Acceptance

Fairness or Equality? Inequality in payments may be seen as inherently unfair, or as appropriate when it reflects differential achievement. Using an economic exchange game, Almås et al. (p. 1176) mapped how judgments changed from 5th-grade students to 13th graders: Fifth graders expressed a preference for equal division of rewards, whereas the 13th graders tolerated unequal outcomes, as long as they had been provided with evidence of unequal inputs. That is, the younger children were strict egalitarians, but the older ones—perhaps as a consequence of exposure to a variety of achievement-based social activities, such as sports—tended toward meritocracy. As children progress to adolescence, their sense of fairness changes from pure equality to proportionality based on merit. Fairness considerations fundamentally affect human behavior, but our understanding of the nature and development of people’s fairness preferences is limited. The dictator game has been the standard experimental design for studying fairness preferences, but it only captures a situation where there is broad agreement that fairness requires equality. In real life, people often disagree on what is fair because they disagree on whether individual achievements, luck, and efficiency considerations of what maximizes total benefits can justify inequalities. We modified the dictator game to capture these features and studied how inequality acceptance develops in adolescence. We found that as children enter adolescence, they increasingly view inequalities reflecting differences in individual achievements, but not luck, as fair, whereas efficiency considerations mainly play a role in late adolescence.
Unconventional s-Wave Superconductivity in Fe(Se,Te)

Breaking Convention The defining characteristics of a superconductor are symmetry of gap function, which tells us something about how pairs of electrons move through the sample, and the strength of that pairing. Together, this information gives us the highest temperature to which the superconductor can remain superconducting. In conventional superconductors the gap function is symmetric, or s-wave, and tends to have low transition temperatures. The newly discovered iron-based superconductors also have s-wave symmetry, but the rather high transition temperatures, in addition to other properties, indicate that they are not conventional. Hanaguri et al. (p. 474; see the Perspective by Hoffman) use scanning tunneling microscopy to provide direct experimental confirmation of the unconventional s-wave pairing of the superconducting carriers in these materials. The electronic gap in an iron-based superconductor has spherically symmetric components that change sign. The superconducting state is characterized by a pairing of electrons with a superconducting gap on the Fermi surface. In iron-based superconductors, an unconventional pairing state has been argued for theoretically. We used scanning tunneling microscopy on Fe(Se,Te) single crystals to image the quasi-particle scattering interference patterns in the superconducting state. By applying a magnetic field to break the time-reversal symmetry, the relative sign of the superconducting gap can be determined from the magnetic-field dependence of quasi-particle scattering amplitudes. Our results indicate that the sign is reversed between the hole and the electron Fermi-surface pockets (s±-wave), favoring the unconventional pairing mechanism associated with spin fluctuations.
Hardware acceleration of combined cipher and forward error correction for low-power wireless applications

Encryption and channel coding are both essential steps for reliable, robust and secure operation within wireless networks. Usually, these algorithms are considered independently of each other because of their antagonism, but solutions exist to combine their features into a single simple primitive. This fusion aims to improve the performance and the energy-efficiency of the wireless device while contributing to the dependability of the whole system. The introduction of a dedicated core implemented on field-programmable logic tightly coupled to the central controller of a wireless sensor node demonstrates further benefits for the energy-efficiency of the system.
mTORC1-Mediated Cell Proliferation, But Not Cell Growth, Controlled by the 4E-BPs

Proliferation Control The protein complex mTORC1, which contains the protein kinase known as mammalian target of rapamycin, is an important regulator of cell proliferation and cell size. Among many targets, mTORC1 phosphorylates the eukaryotic translation initiation factor eIF4E–binding proteins (4E-BPs), thus controlling translation of proteins that regulate proliferation. Dowling et al. (p. 1172) used mice lacking expression of the 4E-BPs to show that these proteins contribute to mTORC1's activation of cell proliferation, but are dispensable for the effects of mTORC1 on cell growth. The latter required another mTORC1 target—the ribosomal protein S6 kinase. mTORC1 inhibitors are being explored as potential anticancer agents, and the presence of 4E-BPs was necessary for mTORC1 inhibitors to reduce the number and size of colonies formed by transformed mouse cells. Control of cell proliferation and cell size is separately regulated in mammals. The mammalian target of rapamycin complex 1 (mTORC1) integrates mitogen and nutrient signals to control cell proliferation and cell size. Hence, mTORC1 is implicated in a large number of human diseases—including diabetes, obesity, heart disease, and cancer—that are characterized by aberrant cell growth and proliferation. Although eukaryotic translation initiation factor 4E–binding proteins (4E-BPs) are critical mediators of mTORC1 function, their precise contribution to mTORC1 signaling and the mechanisms by which they mediate mTORC1 function have remained unclear. We inhibited the mTORC1 pathway in cells lacking 4E-BPs and analyzed the effects on cell size, cell proliferation, and cell cycle progression. Although the 4E-BPs had no effect on cell size, they inhibited cell proliferation by selectively inhibiting the translation of messenger RNAs that encode proliferation-promoting proteins and proteins involved in cell cycle progression. Thus, control of cell size and cell cycle progression appear to be independent in mammalian cells, whereas in lower eukaryotes, 4E-BPs influence both cell growth and proliferation.
Evaluating the performance and scalability of the Ceph distributed storage system

As the data needs in every field continue to grow, storage systems have to grow and therefore need to adapt to the increasing demands of performance, reliability and fault tolerance. This also increases their complexity and costs. Improving the performance and scalability of storage systems while maintaining low costs is thus crucial. The evaluated open source storage system Ceph promises to reliably store data distributed across many nodes. Ceph is targeted at commodity hardware. This study investigates how Ceph performs in different setups and compares this with the theoretical maximum performance of the hardware. We used a bottom-up approach to benchmark Ceph at different architectural levels. We varied the amount of storage nodes and clients to test the scalability of the system. Our experiments revealed that Ceph delivers the promised scalability, and uncovered several points with improvement potential. We observed a significant increase of the write throughput by moving the Ceph journal to a faster location (in memory). Moreover, while the system scaled with the increasing number of clients operating the cluster, we noticed a slight performance degradation after the saturation point. We tested two optimisation strategies - increasing the available RAM or the object size - and noted a write throughput increase of up to 9% and 27%, respectively. Our findings improve the understanding of Ceph and should benefit future users through the presented strategies for tackling various performance limitations.
Induction of Spontaneous Hyaline Cartilage Regeneration Using a Double-Network Gel

Background: A double-network (DN) gel, which was composed of poly-(2-acrylamido-2-methylpropanesulfonic acid) and poly-(N,N′-dimetyl acrylamide) (PAMPS/PDMAAm), has the potential to induce chondrogenesis both in vitro and in vivo. Purpose: To establish the efficacy of a therapeutic strategy for an articular cartilage defect using a DN gel. Study Design: Controlled laboratory study. Methods: A 4.3-mm-diameter osteochondral defect was created in rabbit trochlea. A DN gel plug was implanted into the defect of the right knee so that a defect 2 mm in depth remained after surgery. An untreated defect of the left knee provided control data. The osteochondral defects created were examined by histological and immunohistochemical evaluations, surface assessment using confocal laser scanning microscopy, and real-time polymerase chain reaction (PCR) analysis at 4 and 12 weeks. Samples were quantitatively evaluated with 2 scoring systems reported by Wayne et al and O’Driscoll et al. Results: The DN gel–implanted defect was filled with a sufficient volume of the hyaline cartilage tissue rich in proteoglycan and type 2 collagen. Quantitative evaluation using the grading scales revealed a significantly higher score in the DN gel–implanted defects compared with the untreated control at each period (P < .0001). The mean relative values of type 2 collagen mRNAs in the regenerated tissue were obviously higher in the DN gel–implanted defect than in the untreated control at each period. The mean surface roughness of the untreated control was significantly higher than the normal cartilage at 12 weeks (P = .0106), while there was no statistical difference between the DN gel–implanted and normal knees. Conclusion: This study using the mature rabbit femoral trochlea osteochondral defect model demonstrated that DN gel implantation is an effective treatment to induce cartilage regeneration in vivo without any cultured cells or mammalian-derived scaffolds. Clinical Relevance: This study has prompted us to develop a potential innovative strategy to repair cartilage lesions in the field of joint surgery.