Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans

Plant height (PH) and the number of nodes on the main stem (NN) serve as major plant architecture traits affecting soybean seed yield. Although many quantitative trait loci for the two traits have been reported, their genetic controls at different developmental stages in soybeans remain unclear. Here, 368 soybean breeding lines were genotyped using 62,423 single nucleotide polymorphism (SNP) markers and phenotyped for the two traits at three different developmental stages over two locations in order to identify their quantitative trait nucleotides (QTNs) using compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) approaches. As a result, 11 and 13 QTNs were found by CMLM to be associated with PH and NN, respectively. Among these QTNs, 8, 3, and 4 for PH and 6, 6, and 8 for NN were found at the three stages, and 3 and 6 were repeatedly detected for PH and NN. In addition, 34 and 30 QTNs were found by mrMLM to be associated with PH and NN, respectively. Among these QTNs, 11, 13, and 16 for PH and 11, 15, and 8 for NN were found at the three stages. A majority of these QTNs overlapped with the previously reported loci. Moreover, one QTN within the known E2 locus for flowering time was detected for the two traits at all three stages, and another that overlapped with the Dt1 locus for stem growth habit was also identified for the two traits at the mature stage. This may explain the highly significant correlation between the two traits. Our findings provide evidence for mixed major plus polygenes inheritance for dynamic traits and an extended understanding of their genetic architecture for molecular dissection and breeding utilization in soybeans.
Seroprevalence and herd-level risk factors for seroprevalence of Leptospira spp. in sheep, beef cattle and deer in New Zealand

AIMS To determine seroprevalence of Leptospira borgpetersenii serovar Hardjo and L. interrogans serovar Pomona in beef cattle, sheep and deer in New Zealand and the association between farm-level risk factors and seroprevalence. METHODS Between June 2009 and July 2010, 20 serum samples per flock or herd were collected from 162 sheep flocks, and 116 beef cattle and 99 deer herds from 238 farms, along with farm data by interview. Samples were tested for antibodies to serovars Hardjo and Pomona by microscopic agglutination testing, with a titre ≥48 being positive. Species-specific associations between herd-level seroprevalence (number of seropositive animals, for each serovar, divided by the number of animals tested) and herd-level risk factors were determined by multivariable logistic regression analysis. Vaccinated animals were excluded from seroprevalence estimates but included in multivariable analyses. RESULTS For sheep (n=3,339), animal-level seroprevalence was 43.6 (95% CI=41.9–45.3)% for serovar Hardjo and 14.1 (95% CI=12.9–15.3)% for serovar Pomona; for beef cattle(n=1,886), it was 45.6 (95% CI=43.3–47.9)% for Hardjo and 19.6 (95% CI=17.9–21.5)% for Pomona; and for deer (n=1,870), it was 26.3 (95% CI=24.3–28.4)% for Hardjo, 8.8 (95% CI=7.6–10.2)% for Pomona. In sheep flocks (n=161), flock-level prevalence for Hardjo varied from 77.9–91.3%, and for Pomona from 40.4–73.9%, when ≥1, ≥2 or ≥3 animals were seropositive. In beef herds (n=95), herd-level prevalence for Hardjo varied from 79.0–90.5%, and for Pomona from 42.1–68.4%. In deer herds (n=93), herd-level prevalence for Hardjo varied from 45.2–59.1%, and for Pomona from 22.6–48.4%. For sheep flocks, herd-level seroprevalence for Hardjo was associated with flock size (OR=1.56) and number of dogs (OR=0.75), and for Pomona, seroprevalence varied with region. For beef cattle, herd-level seroprevalence for Hardjo was associated with herd size (OR=1.4), presence of dams (OR=0.6) and vaccination (OR=2.9), and for Pomona, co-grazing with deer (OR=0.4), vaccination (OR=3.22), presence of dams (OR=0.2) and streams (OR=2.7). For deer herds, seroprevalence for Hardjo or Pomona was associated with herd size (OR=1.6 and 1.8) and varied with region, and for Pomona seroprevalence varied with season (summer vs. winter: OR=4.8). CONCLUSIONS Serovars Hardjo and Pomona were highly prevalent at herd and animal levels, with serovar Hardjo highest in all species. Larger herd size was the common risk factor for seroprevalence in all livestock species.
Self-management, self-management support needs and interventions in advanced cancer: a scoping review

Patients with advanced cancer can experience illness trajectories similar to other progressive chronic disease conditions where undertaking self-management (SM) and provision of self-management support (SMS) becomes important. The main objectives of this study were to map the literature of SM strategies and SMS needs of patients with advanced cancer and to describe SMS interventions tested in this patient population. A scoping review of all literature published between 2002 and 2016 was conducted. A total of 11 094 articles were generated for screening from MEDLINE, Embase, PsychINFO, CINAHL and Cochrane Library databases. A final 55 articles were extracted for inclusion in the review. Included studies identified a wide variety of SM behaviours used by patients with advanced cancer including controlling and coping with the physical components of the disease and facilitating emotional and psychosocial adjustments to a life-limiting illness. Studies also described a wide range of SMS needs, SMS interventions and their effectiveness in this patient population. Findings suggest that SMS interventions addressing SMS needs should be based on a sound understanding of the core skills required for effective SM and theoretical and conceptual frameworks. Future research should examine how a patient-oriented SMS approach can be incorporated into existing models of care delivery and the effects of SMS on quality of life and health system utilisation in this population.
68Ga-PSMA PET/CT and PET/MRI in high-risk prostate cancer patients

Treatment of high-risk prostate cancer (HRPCa) is challenging. Local staging and metastatic evaluation are important for the patient management. Recently, prostate-specific membrane antigen (PSMA)-based imaging modalities such as PSMA PET/CT and PET/MRI have received significant attention for detection of recurrent prostate cancer sites with elevated prostate-specific antigen levels, after therapy. Current evidence suggests that these imaging modalities may also have a role for the management of patients with HRPCa. In this review, we discuss PSMA-based imaging modalities in the management of patients with HRPCa.
LETTERS Decreasing Reliability and Increasing Synchroneity of Western North American Streamflow

Assessing climate-related societal vulnerability and mitigating impacts requires timely diagnosis of the nature of regional hydrologic change. A late-twentieth-century emergent trend is discovered toward increasing year-to-year variance (decreasing reliability) of streamflow across the major river basins in western North America—–Fraser, Columbia, Sacramento–San Joaquin, and Upper Colorado. Simultaneously, a disproportionate increase in the incidence of synchronous flows (simultaneous high or low flows across all four river basins) has resulted in expansive water resources stress. The observed trends have analogs in wintertime atmospheric circulation regimes and ocean temperatures, raising new questions on the detection, attribution, and projection of regional hydrologic change induced by climate.
An Empirical Study of Flaky Tests in Android Apps

A flaky test is a test that may fail or pass for the same code under testing (CUT). Flaky tests could be harmful to developers because the non-deterministic test outcome is not reliable and developers cannot easily debug the code. A prior study characterized the root causes and fixing strategies of flaky tests by analyzing commits of 51 Apache open source projects, without analyzing any Android app. Due to the popular usage of Android devices and the multitude of interactions of Android apps with third-party software libraries, hardware, network, and users, we were curious to find if the Android apps manifested unique flakiness patterns and called for any special resolution for flaky tests as compared to the existing literature. For this paper, we conducted an empirical study to characterize the flaky tests in Android apps. By classifying the root causes and fixing strategies of flakiness, we aimed to investigate how our proposed characterization for flakiness in Android apps varies from prior findings, and whether there are domain-specific flakiness patterns. After mining GitHub, we found 29 Android projects containing 77 commits that were relevant to flakiness. We identified five root causes of Android apps' flakiness. We revealed three novel causes - Dependency, Program Logic, and UI. Five types of resolution strategies were observed to address the flaky behavior. Many of the examined commits show developers' attempt to fix flakiness by changing software implementation in various ways. However, there are still 13% commits that simply skipped or removed the flaky tests. Our observations provide useful insights for future research on flaky tests of Android apps.
Analysis of HIV-1 latent reservoir and rebound viruses in a clinical trial of anti-HIV-1 antibody 3 BNC 117 Running Title : Latent and rebound viruses in a trial of 3 BNC 117

A clinical trial was performed to evaluate 3BNC117, a potent anti-HIV-1 antibody, in infected individuals during suppressive antiretroviral therapy (ART) and subsequent analytical treatment interruption (ATI). The circulating reservoir was evaluated by quantitative and qualitative outgrowth assay (QVOA) at entry and after 6 months, prior to ATI. Although there were no significant quantitative changes in the size of the reservoir, the composition of circulating reservoir clones varied over the 6-month period before treatment interruption in a manner that did not correlate with antibody sensitivity. The neutralization profile obtained from the reservoir by QVOA was predictive of time to rebound after ATI, and thus of antibody efficacy. Although 3BNC117 binding site amino acid variants found in rebound viruses pre-existed in the latent reservoir, only 3 of 217 rebound viruses were identical to 868 latent viruses. Instead many of the rebound viruses appeared to be recombinants, even in individuals with resistant reservoir viruses. By incorporating the possibility of recombination, 63% of the rebound viruses could have derived from the observed latent reservoir. In conclusion, viruses emerging during ATI in individuals treated with 3BNC117 are not the dominant species found in the circulating reservoir, but instead appear to represent recombinants. peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi. org/10.1101/324509 doi: bioRxiv preprint first posted online May. 25, 2018;
RADIO IMAGING OBSERVATIONS OF PSR J1023+0038 IN AN LMXB STATE

The transitional millisecond pulsar (MSP) binary system PSR J1023+0038 re-entered an accreting state in 2013 June in which it bears many similarities to low-mass X-ray binaries (LMXBs) in quiescence or near-quiescence. At a distance of just 1.37 kpc, PSR J1023+0038 offers an unsurpassed ability to study low-level accretion onto a highly magnetized compact object. We have monitored PSR J1023+0038 intensively using radio imaging with the Karl G. Jansky Very Large Array, the European VLBI Network and the Low Frequency Array, seeing rapidly variable, flat spectrum emission that persists over a period of six months. The flat spectrum and variability are indicative of synchrotron emission originating in an outflow from the system, most likely in the form of a compact, partially self-absorbed jet, as is seen in LMXBs at higher accretion rates. The radio brightness, however, greatly exceeds extrapolations made from observations of more vigorously accreting neutron star LMXB systems. We postulate that PSR J1023+0038 is undergoing radiatively inefficient “propeller-mode” accretion, with the jet carrying away a dominant fraction of the liberated accretion luminosity. We confirm that the enhanced γ-ray emission seen in PSR J1023+0038 since it re-entered an accreting state has been maintained; the increased γ-ray emission in this state can also potentially be associated with propeller-mode accretion. Similar accretion modes can be invoked to explain the radio and X-ray properties of the other two known transitional MSP systems XSS J12270–4859 and PSR J1824–2452I (M28I), suggesting that radiatively inefficient accretion may be a ubiquitous phenomenon among (at least one class of) neutron star binaries at low accretion rates.
Environmental stress mediates trophic cascade strength and resistance to invasion

Although much attention has focused on the drivers of trophic cascade strength among systems (e.g., habitat type, body size, predator, and prey thermy) comparatively little is known of how trophic cascades change within systems, especially with respect to gradients in environmental stress. To address this, we measured the strength of a trophic cascade across an estuarine stress gradient and tested the predictions of “consumer stress model” that suggests sensitivity to stress is greater in mobile consumers relative to sessile prey. We used field observations and experimental manipulations within a central California estuary (Tomales Bay), where higher water temperatures in summer/fall and lower salinity during winter/ spring may differentially affect predators (native crabs), mesoconsumers (invasive oyster drills), and sessile prey (native oysters). Our results demonstrate that sites with high environmental stress (warmer and lower salinity waters) excluded top predators from the food web, which facilitated high densities of oyster drills and resulted in low oyster survival. In contrast, less stressful sites (cooler and higher salinity waters) had high crab densities leading to reduced oyster drill survival and high oyster survival (an indirect positive effect). Observational data from 14 field sites along both margins of Tomales Bay are consistent with the results of experimental manipulations. This study highlights the importance of environmental stress in mediating within system trophic cascade strength by altering top predator abundance. Our results support the predictions of the consumer stress model and suggest that increasing environmental stress (warming and variable salinity regimes) as a result of climate change may decouple species interactions. Furthermore, warming and extreme low salinities may indirectly intensify the negative effects of nonnative species by reducing the biotic resistance provided by native predators.
Machine Learning-Based Sentiment Analysis for Twitter Accounts

Growth in the area of opinion mining and sentiment analysis has been rapid and aims to explore the opinions or text present on different platforms of social media through machine-learning techniques with sentiment, subjectivity analysis or polarity calculations. Despite the use of various machine-learning techniques and tools for sentiment analysis during elections, there is a dire need for a state-of-the-art approach. To deal with these challenges, the contribution of this paper includes the adoption of a hybrid approach that involves a sentiment analyzer that includes machine learning. Moreover, this paper also provides a comparison of techniques of sentiment analysis in the analysis of political views by applying supervised machine-learning algorithms such as Naive Bayes and support vector machines (SVM).
Knowledge, attitude and practice about hypertension among adult people of selected areas of Bangladesh

Hypertension is a worldwide public-health challenge because of its high frequency and related risks of cardiovascular and kidney disease.1 It has been identified as the prominent risk factor for mortality and is ranked third as a cause of disability-adjusted lifeyears. 2 Most people with hypertension have no symptoms at all; this is why it is known as the “silent killer”. 3 Bangladesh is in the midst of an epidemiologic transition. This country is starting to observe a shift in the major causes of death from mainly infectious diseases and nutritional deficiencies to those due to chronic diseases. The scant population-based data available indicate that prevalence of hypertension in Bangladesh is increasing. Moreover, in Bangladesh, about 85% of total population lives in villages. They are not interested to go to physicians when they become sick due to their poor socioeconomic condition, life style as well as due to lack of awareness.4 Therefore in villages undetected and untreated hypertensive patients are more. The proportion of hypertension among rural population is still undetected though this has strong impact on physical, mental and social burden. It can be dangerous to ignore such symptoms, but neither can they be relied upon to signify hypertension. Hypertension is a serious warning sign. The condition can be a silent killer and it is important for everybody to know their blood pressure reading. If hypertension is detected early, it is possible to minimize the risk of heart attack, heart failure, stroke and kidney failure. As with other non-communicable diseases, self-care can facilitate early detection of hypertension, adherence to medication and healthy behaviors, better control and awareness of the importance of seeking medical advice when necessary. Self-care is important for all, but it is particularly so for people who have limited access to health services due to geographic, physical or economic reasons. Also, this research may facilitate the visibility of this community to policy makers, NGO workers and donors, therefore increasing understanding of the main causes of hypertension. In addition, my research can be an attempt to fill the gap of resources for upcoming researchers and contribute to academic discourse on hypertension.
Recent Advances in High-Frequency Oscillations and Seizure Onset Detection Using Laplacian Electroencephalography via Tripolar Concentric Ring Electrodes

Laplacian electroencephalogram signal from novel and noninvasive tripolar concentric ring electrodes has been demonstrated to have superior performance compared to the electroencephalogram from conventional disc electrodes due to its unique capabilities which allow automatic attenuation of common movement and muscle artifacts in applications including brain-computer interface, seizure onset detection, and detection of high-frequency oscillations and seizure onset zones. This review paper covers the recent advances in the fields of high-frequency oscillations and seizure onset detection based on tripolar Laplacian electroencephalography in animal models and human data to improve the diagnostic yield of electroencephalography for epilepsy. Progression of methodologies utilized including integration of multiple sensors using exponentially embedded families and results obtained including a comparison to the results of others as well as to the performance of the same detector on simultaneously recorded electroencephalogram via conventional disc electrodes is discussed in detail. Specific advantages of using this particular sensor for these particular applications are highlighted. Promising directions for the future work and an overview of currently ongoing research are discussed along with the potential of combining the two detectors and using automatically detected high-frequency oscillations that have been shown to be indicative of early seizure development as auxiliary features for the seizure onset detection.
Couples affected by dementia and their experiences of advance care planning: a grounded theory study

Abstract Global policy places emphasis on the implementation and usage of advance care planning (ACP) to inform decision making at the end of life. For people with dementia, where its use is encouraged at the point of diagnosis, utilisation of ACP is relatively poor, particularly in parts of Europe. Using a constructivist grounded theory methodology, this study explores the ways in which co-residing couples considered ACP. Specifically, it seeks to understand the ways in which people with dementia and their long-term co-residing partners consider and plan, or do not plan, for future medical and social care. Sixteen participants were interviewed. They identified the importance of relationships in the process of planning alongside an absence of formal service support and as a result few engaged in ACP. The study recognises the fundamental challenges for couples in being obliged to consider end-of-life issues whilst making efforts to ‘live well’. Importantly, the paper identifies features of the ACP experience of a relational and biographical nature. The paper challenges the relevance of current global policy and practice, concluding that what is evident is a process of ‘emergent planning’ through which couples build upon their knowledge of dementia, their networks and relationships, and a number of ‘tipping points’ leading them to ACP. The relational and collective nature of future planning is also emphasised.
A Comparison of Borrowing and Default Behaviour Between Men and Women

Abstract Micro-credit started out as an intervention designed to address credit scarcity of women, purportedly because women are disenfranchised from property rights and adhere to repayment norms. Men, in contrast, were known for misusing the loans and defaulting on them. This paper, based on a sample of 490 men and 349 women drawn from four districts in erstwhile Andhra Pradesh, compares the borrowing and default drivers of men and women using systematic sampling techniques and rigorous statistical tests. Results show women’s disenfranchisement from family income and property, and hence their dependence on SHG membership for borrowing. Furthermore, men borrow from banks and planned repayments even in conditions of distress, where both genders are cost rationed. The findings also point to men co-opting with women for financing agriculture. A comparison of default drivers points to debt traps and lower or inadequate income driving defaults and underscores the asymmetry of information and asymmetry of power between lender–principals and borrower–agents, where the principals have an advantage over the agents in both the cases (Saam, 2007). The paper, therefore, questions the blanket assumptions of compliant repayments by women and wilful defaults by men. JEL codes: D63, D82, J16, Z13, C51
Loss of the Wnt/β-catenin pathway in microglia of the developing brain drives pro-inflammatory activation leading to white matter injury

Microglia of the developing brain have unique functional properties but how their activation states is regulated is poorly understood. Inflammatory activation of microglia in the still-developing brain of preterm born infants is associated with permanent neurological sequelae in 9 million infants every year. Investigating the regulators of microglial activation in the developing brain with multiple models of neuroinflammation-mediated injury and primary human microglia we found that a reduction in Wnt/β-catenin signalling is necessary and sufficient to drive an oligodendrocyte-injurious microglial phenotype. We validated in a cohort of preterm born infants that genomic variation in the WNT pathway is associated with the levels of connectivity found in their brains. Using a Wnt agonist delivered by a BBB penetrant microglia-specific targeting nanocarrier we prevented in our animal model the pro-inflammatory microglial activation, white matter injury and behavioural deficits. Collectively, these data validate that the Wnt pathway regulates microglial activation, is critical in the evolution of an important form of human brain injury and is a viable therapeutic target.