Miracle-dz/UniFAR-FTUs huggingface dataset:
The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes

Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of an SVA retrotransposon reporter. By using naïve versus primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development. Although the HUSH component FAM208A binds to endogenous retroviruses (ERVs) and long interspersed element-1s (LINE-1s or L1s), it is mainly required to repress evolutionarily young L1s (mouse-specific lineages <5 million years old). TRIM28, in contrast, is necessary to repress both ERVs and young L1s. Genes co-repressed by TRIM28 and FAM208A are evolutionarily young, or exhibit tissue-specific expression, are enriched in young L1s, and display evidence for regulation through LTR promoters. Finally, we demonstrate that the HUSH complex is also required to repress L1 elements in human cells. Overall, these data indicate that the HUSH complex and TRIM28 co-repress young retrotransposons and new genes rewired by retrotransposon noncoding DNA.
Oil and Macroeconomic Fluctuations in Mexico

This paper tests the conventional contention that, due to the major policy changes in Mexico that stem from the 1980s, fluctuations in the international oil market have had no significant impact on movements in the Mexican economy in the last two decades. It does this by using univariate statistical techniques in its first part and resorting to an econometric structural break test and impulse response analysis respectively in its last two parts. Its findings bear out conventional wisdom: Mexico cannot be likened to an OPEC Country in any respect, including the point of view that its public finance is totally impervious to fluctuations in its oil revenue.
Optimal Harvesting of Age-structured Fish Populations

Abstract A generic age-structured model for optimal harvesting is formulated and analyzed. The aim is to maximize utility from the harvest, net of effort cost. Yield depends on effort, catchability, and population age structure. The recruitment function is nonlinear. The age-structured model can be viewed as a generalization of the biomass approach. Comparison with the biomass model shows that the age-structured information influences the optimal steady-state population and harvest and the qualitative features of optimal transition. Pulse fishing or interior limit cycles are possible, but the optimal solution may represent a smooth, sustainable harvest even when the model is linear in effort. Linearity assumptions do not guarantee the optimality of constant escapement. If the age distribution is dominated by young age classes, the optimal yield may be lower with higher biomass. With knife-edge selectivity, the optimal steady state may become independent of the interest rate. JEL Classification Codes: Q22, Q57, C61
Parent reported outcomes of quality care and satisfaction in the context of a life-limiting fetal diagnosis

Abstract Objective: To identify which quality indicators (QI) predict patient satisfaction. Methods: A cross-sectional design using a validated tool was administered using a Web-based platform. Parents (n = 405) who experienced a life-limiting fetal diagnosis and opted to continue their pregnancy provided feedback on 37 QI and satisfaction with prenatal care. Descriptive analyses and logistic regression identified relationships among variables. Results: Parental satisfaction with care was 75.6%. Statistically significant differences in mean scores were reported with satisfied patients reporting higher agreement with quality indicators. Parents who were satisfied with their care had 1.9 times the odds of reporting that consistent care was provided (CI: 1.4–2.4, p < 0.01), 1.8 times the odds of reporting compassionate care (CI: 1.4–2.5, p < 0.01) and 1.8 times the odds that they received help to cope with their emotions (CI: 1.4–2.3, p < 0.01). The model correctly predicted parent satisfaction 92% of the time. Conclusion: Provision of consistent prenatal care is an important quality indicator for this population of parents. The odds of securing satisfied parents increase when families are treated with compassion and given resources to help them cope with the emotionally devastating experiences associated with a life-limiting fetal diagnosis.
Comparing Terrestrial Laser Scanning (TLS) and Wearable Laser Scanning (WLS) for Individual Tree Modeling at Plot Level

This study presents a comparison between the use of wearable laser scanning (WLS) and terrestrial laser scanning (TLS) devices for automatic tree detection with an estimation of two dendrometric variables: diameter at breast height (DBH) and total tree height (TH). Operative processes for data collection and automatic forest inventory are described in detail. The approach used is based on the clustering of points belonging to each individual tree, the isolation of the trunks, the iterative fitting of circles for the DBH calculation and the computation of the TH of each tree. TLS and WLS point clouds were compared by the statistical analysis of both estimated forest dendrometric parameters and the possible presence of bias. Results show that the apparent differences in point density and relative precision between both 3D forest models do not affect tree detection and DBH estimation. Nevertheless, tree height estimation using WLS appears to be affected by the limited scanning range of the WLS used in this study. TH estimations for trees below a certain height are equivalent using WLS or TLS, whereas TH of taller trees is clearly underestimated using WLS.
Spatio-Temporal Variable Selection Based Support Vector Regression for Urban Traffic Flow Prediction

Short-term urban traffic flow prediction remains a difficult yet important problem in the intelligent transportation systems (ITS). Most previous spatio-temporal based urban traffic flow prediction techniques just pay attention to building the relationship between the adjacent upstream and downstream road segments using various models. While in this paper, we take advantage of the spatial and temporal information from all available road segments in the road network to predict the short-term traffic volume accurately. However, the available traffic states can be high-dimensional for high-density or large scale road networks. Therefore, we present a spatio-temporal variable selection based support vector regression (VS-SVR) model fed with the high-dimensional traffic data collected from all available road segments. Our prediction framework can be presented as a two-stage model. In the first stage, we employ the multivariate adaptive regression splines (MARS) model to select a set of predictors most related to the target one from the high-dimensional spatio-temporal variables, and reasonable weights are assigned to the selected predictors. In the second stage, the kernel learning method, support vector regression (SVR), is trained on the weighted variables in the second stage for prediction. In the experiments, we employ the actual traffic volume collected from a subarea of Shanghai, China, every 10 minutes. The experimental results indicate that the proposed spatio-temporal variable selection based support vector regression model can generate preferable results in contrast with the time series based autoregression (AR) method, the separate MARS model, and the SVR model.
The british association of surgical oncology

I AM CONSCIOUS of the historic importance of this first meeting of the Association here in the Royal College of Surgeons of England, and of the privilege of addressing you. The objectives of our new Association, with the methods that we visualize to achieve them, would have stirred the imagination and elicited the approbation of John Hunter, whose mind and work ranged throughout the whole realm of biology-a subject which is also of vital concern to the surgical oncologist. No one who has witnessed the remarkable accretions to biological knowledge during the past 25 years could be immune from feeling that we stand today on the fringe of discoveries which will exert a profound influence on our understanding and management of disease processes, including those of neoplasia. The time is opportune, therefore, to coalesce various arts and sciences by a new and determined effort in order to find solutions to some of the most profound biological problems presented in oncology.
Waist circumference and the metabolic syndrome predict the development of elevated albuminuria in non-diabetic subjects: the DESIR Study

Objective Metabolic determinants of microalbuminuria remain poorly understood in non-diabetic individuals and particularly in women. We investigated in both sexes whether an elevated waist circumference (WC) or the presence of the metabolic syndrome (MetS) predict the development of elevated albuminuria at 6 years. Design and patients We studied 2738 subjects from the DESIR cohort without microalbuminuria or diabetes at baseline and who were followed up for 6 years. Results At 6 years, 254 individuals [9.3%; 95% confidence interval (CI) 8.2–10.4%] had developed elevated albuminuria (≥ 20 mg/l), which was significantly and positively associated with WC and blood pressure, but not with fasting glucose, lipids or body mass index in either sex. In both sexes, subjects with a high WC or with MetS at baseline were more likely to develop elevated albuminuria at 6 years compared with those with a normal WC or absence of MetS. In multivariate logistic analysis, WC as a continuous variable or a WC of 94 cm or greater for men and a WC greater than 88 cm for women were predictive of the development of elevated albuminuria, after adjusting for age, hypertension, the use of angiotensin-converting enzyme inhibitors, fibrinogen and glycaemia. MetS was a risk factor for elevated albuminuria in men (odds ratio 1.87; 95% CI 1.25–2.81), with differences according to the MetS definition. Conclusion Abdominal adiposity is related to the development of elevated albuminuria in both sexes, suggesting that the measurement of WC may improve the identification of non-diabetic individuals at risk of developing microalbuminuria and emphasizing the interest of screening for albuminuria among those with MetS.
Morbillivirus and henipavirus attachment protein cytoplasmic domains differently affect protein expression, fusion support and particle assembly

The amino-terminal cytoplasmic domains of paramyxovirus attachment glycoproteins include trafficking signals that influence protein processing and cell surface expression. To characterize the role of the cytoplasmic domain in protein expression, fusion support and particle assembly in more detail, we constructed chimeric Nipah virus (NiV) glycoprotein (G) and canine distemper virus (CDV) haemagglutinin (H) proteins carrying the respective heterologous cytoplasmic domain, as well as a series of mutants with progressive deletions in this domain. CDV H retained fusion function and was normally expressed on the cell surface with a heterologous cytoplasmic domain, while the expression and fusion support of NiV G was dramatically decreased when its cytoplasmic domain was replaced with that of CDV H. The cell surface expression and fusion support functions of CDV H were relatively insensitive to cytoplasmic domain deletions, while short deletions in the corresponding region of NiV G dramatically decreased both. In addition, the first 10 residues of the CDV H cytoplasmic domain strongly influence its incorporation into virus-like particles formed by the CDV matrix (M) protein, while the co-expression of NiV M with NiV G had no significant effect on incorporation of G into particles. The cytoplasmic domains of both the CDV H and NiV G proteins thus contribute differently to the virus life cycle.
Contracts, hold-up and labor markets

The implications for labor markets of contracts to avoid hold-up of investments are assessed. Employment at will protects the returns on a firm's general and specific investments without wages increasing with tenure. With turnover costs, fixed but renegotiable wages can protect general investments by both firm and employee, and generage wage stickiness without adversely affecting employment. Employment contracts that induce efficient specific investments by both firm and employee are problematic so it makes sense, wherever possible, for one side to make all such investments. With private information, fixed wages may induce fewer inefficient separations than employment at will.
Molecular epidemiology of the plasmid-encoded TEM-1 β-lactamase in Scotland

SUMMARY A survey of the β-lactamases responsible for ampicillin resistance in urinary Escherichia coli isolated in central Scotland has been performed. The TEM-1 β-lactamase was found to be most prevalent occurring in 88.2% of ampicillin-resistant isolates tested. Forty-six percent of the TEM-1 producing strains were able to transfer this resistance to E. coli J62–2 at 37 ° C. Analysis of the resulting transconjugants revealed that the degree of resistance to amoxycillin and amoxycillin in combination with clavulanic acid was related to the specific activity of the TEM-1 β-lactamase. The variation in specific activity was shown to be related to plasmid type as determined by restriction analysis. No obvious relationship between β-lactamase specific activity and resistance to amoxycillin and amoxycillin plus clavulanic acid could be demonstrated in the original plasmid donor strains.
VSE-ens: Visual-Semantic Embeddings with Efficient Negative Sampling

Jointing visual-semantic embeddings (VSE) have become a research hotpot for the task of image annotation, which suffers from the issue of semantic gap, i.e., the gap between images' visual features (low-level) and labels' semantic features (high-level). This issue will be even more challenging if visual features cannot be retrieved from images, that is, when images are only denoted by numerical IDs as given in some real datasets. The typical way of existing VSE methods is to perform a uniform sampling method for negative examples that violate the ranking order against positive examples, which requires a time-consuming search in the whole label space. In this paper, we propose a fast adaptive negative sampler that can work well in the settings of no figure pixels available. Our sampling strategy is to choose the negative examples that are most likely to meet the requirements of violation according to the latent factors of images. In this way, our approach can linearly scale up to large datasets. The experiments demonstrate that our approach converges 5.02x faster than the state-of-the-art approaches on OpenImages, 2.5x on IAPR-TCI2 and 2.06x on NUS-WIDE datasets, as well as better ranking accuracy across datasets.
Regression Analysis of Doubly Censored Failure Time Data with Applications to AIDS Studies

Summary. In many epidemiological studies, the survival time of interest is the elapsed time between two related events, the originating event and the failure event, and the times of the occurrences of both events are right or interval censored. We discuss the regression analysis of such studies and a simple estimating equation approach is proposed under the proportional hazards model. The method can easily be implemented and does not involve any iteration among unknown parameters, as full likelihood approaches proposed in the literature do. The asymptotic properties of the proposed regression coefficient estimates are derived and an AIDS cohort study is analyzed to illustrate the proposed approach.
Factors predicting early recurrence after transanal endoscopic microsurgery excision for rectal adenoma

Introduction Transanal endoscopic microsurgery (TEM) is an accepted way of excising rectal adenomas with low morbidity and mortality, avoiding major resectional surgery. However, there are no agreed criteria for surveillance following TEM. The purpose of this study was to identify criteria to guide surveillance programmes, thus reducing the surveillance burden for those patients at low risk of recurrence.
Relational Timing in the Production and Perception of Japanese Singleton and Geminate Stops

Abstract This work examines the production and perception of the Japanese singleton versus geminate stop contrast in order to investigate properties that distinguish the contrast in the face of variability due to speech rate. The acoustic study found two local relational durations, the ratio of the stop to the preceding mora and the ratio of the stop to the following vowel, to be stable across speaking rates and to accurately classify singleton and geminate productions. However, the subsequent perception study demonstrated an influential role of the preceding mora duration and a marginal role of the following vowel duration on listeners’ categorization. These results demonstrate that Japanese listeners can take advantage of relative duration in the perception of the stop length contrast, and that relative strength of simultaneously available acoustic cues does not necessarily translate into equal perceptual importance.
Sliding mode heading control of an overactuated, hover‐capable autonomous underwater vehicle with experimental verification

A sliding mode heading control system is developed for overactuated, hover‐capable autonomous underwater vehicles (AUVs) operating over a range of forward speeds. A simplified switching function is introduced, and simulation studies are proposed accordingly. The results with this novel switching function show a significant improvement in the chattering problem when compared to other conventional switching function candidates. Studies on sensitivities to a range of hydrodynamic parameter uncertainties are presented, and the parameters that have major influences on the sliding mode control performance are highlighted. The proposed control system is also proven in the field trials to enhance vehicle response, yielding consistent, and robust performance over the entire range of vehicle's speeds, even when subjected to external disturbance. It also shows superior heading tracking performance when compared to a proportional‐derivative (PD) based approach implemented on the same vehicle. However, this improved performance requires intense control actions as a trade‐off, causing the AUV to expend more energy than with the P‐D approach. Path following trials, where the AUV is demanded to follow a set of GPS coordinates at the water surface, are presented. These demonstrate the applicability of the proposed heading control system in a practical operation. The presented SMC scheme can be applied to any vehicle straightforwardly, but the control allocation part may need to be modified regarding the actuator configuration of that vehicle.
A Fully On-Chip 80-pJ/b OOK Super-Regenerative Receiver With Sensitivity-Data Rate Tradeoff Capability

This paper presents an ultra-low power super-regenerative receiver suitable for ON–OFF keying modulation and provides analytical insight into its design procedure. The receiver is fabricated in 40-nm CMOS technology and operates in the ISM band of 902–928 MHz. Binary search algorithm through successive approximation register architecture is being exploited to calibrate the internally generated quench signal and the working frequency of the receiver. Employing an on-chip inductor and a single ended to differential architecture for the input amplifier has made the receiver fully integrable, eliminating the need for external components. A power consumption of 320 $\mu \text{W}$ from a 0.65-V supply results in an excellent energy efficiency of 80 pJ/b at 4-Mb/s data rate (DR). The receiver also employs an analog to digital converter that enables soft-decisioning and a convenient sensitivity-DR tradeoff, achieving sensitivity of −86.5, and −101.5 dBm at 1000- and 31.25-kbps DR, respectively.
Undiagnosed Illness and Neuropsychiatric Behaviors in Community Residing Older Adults With Dementia

The aim of this retrospective analysis was to examine prevalence of undiagnosed acute illness and characteristics including neuropsychiatric symptoms associated with illness in community residing older adults with Alzheimer disease or related disorders. Subjects included 265 community residing older adults with dementia who participated in 1 of 2 interventions being tested in randomized clinical trials. Measures included a brief nursing assessment and laboratory evaluations including complete blood count, blood chemistry (Chem 7), and thyroid function tests of serum samples and culture and sensitivity tests of urine samples. Undiagnosed illness was identified according to currently published criteria. Neuropsychiatric behaviors were assessed using 21 behaviors derived from standard measures. Thirty-six percent (N=96) of patients had clinical findings indicative of undetected illness. Conditions most prevalent were bacteriuria (15%), followed by hyperglycemia (6%) and anemia (5%). The behavior most often demonstrated among those with detected illness was resisting or refusing care (66% vs. 47% for those without detected illness). Individuals with detected illness had significantly lower functional status scores [3.8 vs. 4.4, t(275)=7.01, P=0.01], lower cognitive status scores [10.5 vs. 14.4, t(275)=12.1, P<0.01], and were more likely to be prescribed psychotropic medications for behavior (41% vs. 26%, &khgr;2=3.67, P<0.05) than those without illness. Findings suggest that challenges of diagnosing acute illness with atypical presentation must be addressed to promote quality of care and the specialized needs for this vulnerable population.
Assessing the Communication Issues Involved in Implemening High-Level Behaviors in Unmanned Aerial Vehicles

Unmanned aerial vehicles (UAVs) are used in many applications, both military and civilian. There is a push by researchers to implement coordinated behaviors in groups of autonomous UAVs. Such coordinated behavior requires a reliable degree of communication between cooperating aircraft. Therefore, this research examines one such group behavior, namely formation flight, from a network standpoint. A mobility model is described that represents stressful flying conditions, and a series of simulations are run to explore the network constraints that are placed on a formation of flying autonomous UAVs. The results of these simulations are useful for UAV operators to know the limits of the formation from a wireless network standpoint. Furthermore, these simulations provide a starting point for further research into protocols that can yield improved results
State Roles in Providing Affordable Mass Transport Services for Low-Income Residents

Governments support urban mass transport services worldwide under the guise of helping the poor and improving the environment. With more and more governments cash-strapped and facing budgetary shortfalls in other vital areas, the fiscal burdens of underwriting public transport have prompted some observers to question such rationales. This paper reviews the role of states in ensuring affordable mass transport services are available to low-income residents. The heavy financial burdens that the poor sometime face in moving about the city and possible ways of reducing these impacts are discussed. Examples of keeping transit fares affordable while also ensuring reasonably cost-effective mass transport services are cited. Because public policy choices that shape mass transport services are informed by technical evaluations, this paper also examines conventional practices regarding how transport proposals are reviewed and assessed. It argues that moving toward a framework that focuses on enhancing accessibility rather than principally mobility would better represent the long-term impacts of capital investments while also promoting the interests of mobility-disadvantaged populations.