Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust analysis of related samples under the presence of population substructure

We propose a new method for genome-wide association analysis with a family-based design. The proposed method is robust against population substructure while it is more efficient than the traditional method such as transmission disequilibrium test for related samples. The proposed method estimates the correlation matrix between individuals and then the principal component analysis is applied. To maximize the statistical power, we consider the additive polygenic model and a best linear unbiased predictor is used as offset. We confirmed that the proposed method is always efficient by simulation studies. The method will be applied to Framingham Heart study.
Timing-based mutual exclusion

The benefits that can be obtained by using timing information in mutual exclusion algorithms are examined. A simple and efficient timing-based mutual exclusion algorithm is given. This algorithm always guarantees mutual exclusion (i.e. even when run asynchronously) and also avoids deadlock in case certain (realistic) inexact timing constraints are met. The algorithm uses only two shared read/write registers (a total of log n+1 bits), thus overcoming the n register lower bound for asynchronous algorithms. It is proved that the problem cannot be solved with only one shared register, so that this algorithm is optimal in terms of the number of registers. A lower bound is proved for the time complexity of any deadlock-free mutual exclusion protocol, as a function of the number of shared registers it employs. This bound shows that the algorithm described is near optimal, in terms of time complexity. It is shown that two natural ways of weakening the timing assumptions lead (unfortunately) to an n register lower bound. <<ETX>>
Patterns of Diversity in Marine Phytoplankton

Diversity Gradients Latitudinal gradients in species abundance, with relatively few occurring at the poles and many at the equator, are well known for macroorganisms. It is a matter of controversy, fueled by a lack of observational data, whether such gradients also occur among microorganisms. Barton et al. (p. 1509, published online 25 February) have built on a global marine circulation model to predict the dynamics of phytoplankton populations. In silico, they obtain patterns of latitudinal gradation for plankton that are interspersed with hotspots of amplified diversity, which point to plausible natural explanations for the phenomenon that can be tested in the future by systematic metagenomic surveys. Highest diversity occurs in physically dynamic mid-latitude zones, and lowest diversity and highest biomass occur toward the poles. Spatial diversity gradients are a pervasive feature of life on Earth. We examined a global ocean circulation, biogeochemistry, and ecosystem model that indicated a decrease in phytoplankton diversity with increasing latitude, consistent with observations of many marine and terrestrial taxa. In the modeled subpolar oceans, seasonal variability of the environment led to competitive exclusion of phytoplankton with slower growth rates and lower diversity. The relatively weak seasonality of the stable subtropical and tropical oceans in the global model enabled long exclusion time scales and prolonged coexistence of multiple phytoplankton with comparable fitness. Superimposed on the decline in diversity seen from equator to pole were “hot spots” of enhanced diversity in some regions of energetic ocean circulation, which reflected lateral dispersal.
Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate

Carbon Cycle and Climate Change As climate change accelerates, it is important to know the likely impact of climate change on the carbon cycle (see the Perspective by Reich). Gross primary production (GPP) is a measure of the amount of CO2 removed from the atmosphere every year to fuel photosynthesis. Beer et al. (p. 834, published online 5 July) used a combination of observation and calculation to estimate that the total GPP by terrestrial plants is around 122 billion tons per year; in comparison, burning fossil fuels emits about 7 billion tons annually. Thirty-two percent of this uptake occurs in tropical forests, and precipitation controls carbon uptake in more than 40% of vegetated land. The temperature sensitivity (Q10) of ecosystem respiratory processes is a key determinant of the interaction between climate and the carbon cycle. Mahecha et al. (p. 838, published online 5 July) now show that the Q10 of ecosystem respiration is invariant with respect to mean annual temperature, independent of the analyzed ecosystem type, with a global mean value for Q10 of 1.6. This level of temperature sensitivity suggests a less-pronounced climate sensitivity of the carbon cycle than assumed by recent climate models. A combination of data and models provides an estimate of how much photosynthesis by all the world’s plants occurs each year. Terrestrial gross primary production (GPP) is the largest global CO2 flux driving several ecosystem functions. We provide an observation-based estimate of this flux at 123 ± 8 petagrams of carbon per year (Pg C year−1) using eddy covariance flux data and various diagnostic models. Tropical forests and savannahs account for 60%. GPP over 40% of the vegetated land is associated with precipitation. State-of-the-art process-oriented biosphere models used for climate predictions exhibit a large between-model variation of GPP’s latitudinal patterns and show higher spatial correlations between GPP and precipitation, suggesting the existence of missing processes or feedback mechanisms which attenuate the vegetation response to climate. Our estimates of spatially distributed GPP and its covariation with climate can help improve coupled climate–carbon cycle process models.
SPATA: A highly accurate GUI tool for de novo transcriptome assembly

RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing with algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to read localization, followed by a novel algorithm to de novo read assembly. Availability: the GUI tool is freely available at http://asammate.sourceforge. net/.
Unicellular Cyanobacterial Distributions Broaden the Oceanic N2 Fixation Domain

Oceanic Nitrogen Fixation Nitrogen fixation in the oceans is important in sustaining global marine productivity and balances carbon dioxide export to the deep ocean. It was previously believed that marine nitrogen fixation was due to a single genus of filamentous cyanobacteria, Trichodesmium. The recent discovery of unicellular open-ocean cyanobacteria has raised the question of how they contribute to global ocean nitrogen fixation and how they compare in distribution and activity to Trichodesmium. Using data collected from the southwest Pacific Ocean, Moisander et al. (p. 1512, published online 25 February) show that the unicellular nitrogen-fixing cyanobacteria (UCYN-A and Crocosphaera watsonii) have distinct ecophysiologies and distinct oceanic distributions from each other, and from Trichodesmium. These data can be incorporated into models to retune estimates of the global rates of oceanic nitrogen fixation and carbon sequestration. Nitrogen fixation in the South Pacific Ocean is partitioned among several microbe species with distinct ecophysiologies. Nitrogen (N2)–fixing microorganisms (diazotrophs) are an important source of biologically available fixed N in terrestrial and aquatic ecosystems and control the productivity of oligotrophic ocean ecosystems. We found that two major groups of unicellular N2-fixing cyanobacteria (UCYN) have distinct spatial distributions that differ from those of Trichodesmium, the N2-fixing cyanobacterium previously considered to be the most important contributor to open-ocean N2 fixation. The distributions and activity of the two UCYN groups were separated as a function of depth, temperature, and water column density structure along an 8000-kilometer transect in the South Pacific Ocean. UCYN group A can be found at high abundances at substantially higher latitudes and deeper in subsurface ocean waters than Trichodesmium. These findings have implications for the geographic extent and magnitude of basin-scale oceanic N2 fixation rates.
A better polynomial-time schedulability test for real-time fixed-priority scheduling algorithms

The problem of scheduling real-time periodic task has been studied extensively since its first introduction by C.L. Liu and J.W. Layland in their classic paper (1973). Due to several merits of the fixed-priority scheduling scheme, a lot of research work has focused on the analysis of fixed-priority scheduling algorithms. For the case that the deadlines of the executions of all the tasks coincide with the ends of their corresponding periods. Liu and Layland derived a worst-case utilization bound for a task set to be schedulable by the rate-monotonic (RM) algorithm. A. Burchard et al. (1995) presented another schedulability condition for RM, which has a higher utilization bound under a certain task condition. Although their closed-form utilization bounds provide a convenient way for testing the schedulability of a task set under the RM algorithm, the schedulability test using their bounds is too pessimistic since a lot of task sets with total utilizations larger than their bounds (and less than or equal to 1) are still schedulable by RM. In this paper, we propose a polynomial-time schedulability test and prove that it is better than Liu and Layland's and Burchard's utilization bounds in the sense that as long as the total utilization of a task set is less than or equal to their bounds, our schedulability test will always answer positively for the schedulability of the task set under RM and even if a feasible task set has a total utilization larger than their bounds, our schedulability test will still answer positively with a high probability. We also show how to generalize our polynomial-time schedulability test to handle general task sets scheduled by arbitrary fixed-priority scheduling algorithms.
Meiotic Recombination Provokes Functional Activation of the p53 Regulatory Network

Germline Quality Control The p53 tumor suppressor protein plays a key role in protecting organisms from aberrant cancer cells. But during evolution, animals would rarely, if ever, have lived long enough to develop cancer and so need such a function of p53. What, then, were the original functions for which p53 was selected? Lu et al. (p. 1278) observed a pulse of p53 activation during Drosophila development in the female germ line. In cancer, p53 is activated in response to DNA damage. Similarly, in this study, breaks in DNA that occur normally during meiosis also caused p53 activation. In animals in which resolution of DNA breaks during crossing over was inhibited, activation of p53 was prolonged; furthermore, when p53 was also lacking oogenesis was abnormal. Exactly how activation of p53 contributes to the process of chromosome recombination during meiosis remains unclear, but it may provide quality control, only allowing survival of gametes that possess intact DNA. A tumor suppressor appears to protect against aberrant chromosome breakage during meiosis. The evolutionary appearance of p53 protein probably preceded its role in tumor suppression, suggesting that there may be unappreciated functions for this protein. Using genetic reporters as proxies to follow in vivo activation of the p53 network in Drosophila, we discovered that the process of meiotic recombination instigates programmed activation of p53 in the germ line. Specifically, double-stranded breaks in DNA generated by the topoisomerase Spo11 provoked functional p53 activity, which was prolonged in cells defective for meiotic DNA repair. This intrinsic stimulus for the p53 regulatory network is highly conserved because Spo11-dependent activation of p53 also occurs in mice. Our findings establish a physiological role for p53 in meiosis and suggest that tumor-suppressive functions may have been co-opted from primordial activities linked to recombination.
Knee Function and Prevalence of Knee Osteoarthritis after Anterior Cruciate Ligament Reconstruction

Background Few prospective long-term studies of more than 10 years have reported changes in knee function and radiologic outcomes after anterior cruciate ligament (ACL) reconstruction. Purpose To examine changes in knee function from 6 months to 10 to 15 years after ACL reconstruction and to compare knee function outcomes over time for subjects with isolated ACL injury with those with combined ACL and meniscal injury and/or chondral lesion. Furthermore, the aim was to compare the prevalence of radiographic and symptomatic radiographic knee osteoarthritis between subjects with isolated ACL injuries and those with combined ACL and meniscal and/or chondral lesions 10 to 15 years after ACL reconstruction. Study Design Cohort study; Level of evidence, 2. Methods Follow-up evaluations were performed on 221 subjects at 6 months, 1 year, 2 years, and 10 to 15 years after ACL reconstruction with bone-patellar tendon-bone autograft. Outcome measurements were KT-1000 arthrometer, Lachman and pivot shift tests, Cincinnati knee score, isokinetic muscle strength tests, hop tests, visual analog scale for pain, Tegner activity scale, and the Kellgren and Lawrence classification. Results One hundred eighty-one subjects (82%) were evaluated at the 10- to 15-year follow-up. A significant improvement over time was revealed for all prospective outcomes of knee function. No significant differences in knee function over time were detected between the isolated and combined injury groups. Subjects with combined injury had significantly higher prevalence of radiographic knee osteoarthritis compared with those with isolated injury (80% and 62%, P = .008), but no significant group differences were shown for symptomatic radiographic knee osteoarthritis (46% and 32%, P = .053). Conclusion An overall improvement in knee function outcomes was detected from 6 months to 10 to 15 years after ACL reconstruction for both those with isolated and combined ACL injury, but significantly higher prevalence of radiographic knee osteoarthritis was found for those with combined injuries.
Evolution of an Expanded Sex-Determining Locus in Volvox

Revealing Volvox Female and male gametes of the green alga, Volvox, significantly differ in size. Those of Chlamydomonas, another green algae from a lineage that separated from Volvox some 200 million years ago, are the same size. We know sex in Chlamydomonas is governed by a sex-determining locus called MT. In a detailed comparison of the MT loci of Volvox and Chlamydomonas, Ferris et al. (p. 351) found that although MT has retained some similarity in gene order, its composition has greatly changed between the two species. In Volvox, new genes have been coopted into this locus and show sex-specific expression. Mating loci among green algae show conserved gene order, but also have many unique features that may explain gamete size differences. Although dimorphic sexes have evolved repeatedly in multicellular eukaryotes, their origins are unknown. The mating locus (MT) of the sexually dimorphic multicellular green alga Volvox carteri specifies the production of eggs and sperm and has undergone a remarkable expansion and divergence relative to MT from Chlamydomonas reinhardtii, which is a closely related unicellular species that has equal-sized gametes. Transcriptome analysis revealed a rewired gametic expression program for Volvox MT genes relative to Chlamydomonas and identified multiple gender-specific and sex-regulated transcripts. The retinoblastoma tumor suppressor homolog MAT3 is a Volvox MT gene that displays sexually regulated alternative splicing and evidence of gender-specific selection, both of which are indicative of cooption into the sexual cycle. Thus, sex-determining loci affect the evolution of both sex-related and non–sex-related genes.
Time to Tap Africa's Livestock Genomes

We need to better understand and exploit the genetic diversity of Africa's indigenous livestock breeds—before they fade away. If you travel across rural Africa looking for livestock such as cows, pigs, and goats, rather than scenic or wildlife wonders, you will be struck by the extraordinary diversity of its indigenous breeds (1). But the visual wonders of coat color or horn shape are only the tip of the iceberg. Looking deeper, a world of Darwinian adaptations—from the ability to tolerate parasites to robust milk production—waits to be discovered, understood, and used. The scientific community has largely ignored these adaptations. Now, however, we have the opportunity, by combining genomic and geo-environmental data, to unravel African livestock adaptations and to use this information to aid sustainable breeding improvements and development. But we must act soon: The genetic diversity of Africa's indigenous livestock is now threatened by a range of economic and demographic forces.
Observation of Plasmarons in Quasi-Freestanding Doped Graphene

More Crossings for Graphene Graphene, which consists of single sheets of graphite, has a number of distinctive electronic properties, including a conical structure that leads to a “Dirac point” where the valence and conduction band intersect at a zero-energy point. Bostwick et al. (p. 999) used angle-resolved photoemission spectroscopy to study graphene that was doped with alkali atoms and suspended from its substrate. They observed features associated with plasmarons, which arise from the interaction of the charge carriers with plasmons, the density oscillations of the electron gas. The Dirac crossing now becomes three crossings: one that involves charge bands, one involving plasmarons, and one involving the interaction between the two. Doping of graphene introduces two new crossing points of the conduction and valance-electron bands. A hallmark of graphene is its unusual conical band structure that leads to a zero-energy band gap at a single Dirac crossing point. By measuring the spectral function of charge carriers in quasi-freestanding graphene with angle-resolved photoemission spectroscopy, we showed that at finite doping, this well-known linear Dirac spectrum does not provide a full description of the charge-carrying excitations. We observed composite “plasmaron” particles, which are bound states of charge carriers with plasmons, the density oscillations of the graphene electron gas. The Dirac crossing point is resolved into three crossings: the first between pure charge bands, the second between pure plasmaron bands, and the third a ring-shaped crossing between charge and plasmaron bands.
Network Diversity and Economic Development

Network for Recovery A long-standing theory suggests that social diversity leads to economic development. By combining the United Kingdom's telephone communication records (both landline and mobile) with information on regional economic conditions, Eagle et al. (p. 1029) demonstrate that network diversity alone accounts for over three-quarters of the variance of a region's economic status. Although the data cannot be used to show causality, the association suggests that economic development and recovery may depend not solely on monetary stimulus but also on the development of a nation's social infrastructure. Social diversity is associated with economic development. Social networks form the backbone of social and economic life. Until recently, however, data have not been available to study the social impact of a national network structure. To that end, we combined the most complete record of a national communication network with national census data on the socioeconomic well-being of communities. These data make possible a population-level investigation of the relation between the structure of social networks and access to socioeconomic opportunity. We find that the diversity of individuals’ relationships is strongly correlated with the economic development of communities.
Factors Affecting Healing Rates after Arthroscopic Double-Row Rotator Cuff Repair

Background Double-row arthroscopic rotator cuff repairs were developed to improve initial biomechanical strength of repairs to improve healing rates. Despite biomechanical improvements, failure of healing remains a clinical problem. Purpose To evaluate the anatomical results after double-row arthroscopic rotator cuff repair with ultrasound to determine postoperative repair integrity and the effect of various factors on tendon healing. Study Design Case series; Level of evidence, 4. Methods Forty-eight patients (49 shoulders) who had a complete arthroscopic rotator cuff repair (double-row technique) were evaluated with ultrasound at a minimum of 6 months after surgery. Outcome was evaluated at a minimum of 1-year follow-up with standardized history and physical examination, visual analog scale for pain, active forward elevation, and preoperative and postoperative shoulder scores according to the system of the American Shoulder and Elbow Surgeons and the Simple Shoulder Test. Quantitative strength was measured postoperatively. Results Ultrasound and physical examinations were performed at a minimum of 6 months after surgery (mean, 16 months; range, 6 to 36 months) and outcome questionnaire evaluations at a minimum of 12 months after surgery (mean, 29 months; range, 12 to 55 months). Of 49 repairs, 25 (51%) were healed. Healing rates were 67% in single-tendon tears (16 of 24 shoulders) and 36% in multitendon tears (9 of 25 shoulders). Older age and longer duration of follow-up were correlated with poorer tendon healing (P < .03). Visual analog scale for pain, active forward elevation, American Shoulder and Elbow Surgeons scores, and Simple Shoulder Test scores all had significant improvement from baseline after repair (P < .0001). Conclusion Increased age and longer duration of follow-up were associated with lower healing rates after double-row rotator cuff repair. The biological limitation at the repair site, as reflected by the effects of age on healing, appears to be the most important factor influencing tendon healing, even after maximizing repair biomechanical strength with a double-row construct.