Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive Coding with Neural Transmission Delays: A Real-Time Temporal Alignment Hypothesis

Visual Abstract Hierarchical predictive coding is an influential model of cortical organization, in which sequential hierarchical levels are connected by backward connections carrying predictions, as well as forward connections carrying prediction errors. To date, however, predictive coding models have largely neglected to take into account that neural transmission itself takes time. For a time-varying stimulus, such as a moving object, this means that backward predictions become misaligned with new sensory input. We present an extended model implementing both forward and backward extrapolation mechanisms that realigns backward predictions to minimize prediction error. This realignment has the consequence that neural representations across all hierarchical levels become aligned in real time. Using visual motion as an example, we show that the model is neurally plausible, that it is consistent with evidence of extrapolation mechanisms throughout the visual hierarchy, that it predicts several known motion–position illusions in human observers, and that it provides a solution to the temporal binding problem.
Cardiovascular Health Metrics in the Development and Regression of Nonalcoholic Fatty Liver Disease: A Cohort Study

Cardiovascular Health (CVH) metrics scores are associated with cardiovascular disease but whether CVH scores are associated with nonalcoholic fatty liver disease (NAFLD) is uncertain. Our aim was to investigate associations between CVH scores and development or regression of NAFLD. A cohort study was performed in Korean adults who underwent a comprehensive health examination. The CVH metrics were defined according to the American Heart Association Life’s Simple 7 metrics, ranging from 0 (all metrics considered unhealthy) to 7 (all metrics considered healthy). Fatty liver was diagnosed by ultrasound, and liver fibrosis assessed using NAFLD fibrosis score (NFS). Among 93,500 participants without NAFLD or fibrosis at baseline, 15,899 developed NAFLD, and 998 developed NAFLD plus intermediate/high NFS. Healthy CVH metrics were inversely associated with NAFLD and also NAFLD with fibrosis. In time-dependent models after updating the CVH score and confounders as time-varying covariate, the multivariable-adjusted hazard ratio (95% confidence intervals) for incident NAFLD plus intermediate/high NFS participants with CVH metrics score 2, 3, 4, 5, or 6–7 to those with score 0–1 were 0.86 (0.59–1.25), 0.51 (0.36–0.73), 0.44 (0.31–0.62), 0.20 (0.14–0.29) and 0.09 (0.05–0.14), respectively. Regression of NAFLD occurred in 9742/37,517 participants who had NAFLD at baseline with positive association with CVH metrics. Higher CVH scores were significantly associated with both (a) decreased incidence of NAFLD, and (b) regression of existing NAFLD. Promoting adherence to ideal CVH metrics can be expected to reduce the burden of NAFLD as well as cardiovascular disease.
Optimal zero-forcing precoding design - oversampled FB frame approach

This paper presents a frame analysis of Zero Forcing (ZF) precoding problem. It shows that from a frame point of view, the filter bank (FB) channel is a synthesis frame and its canonical dual analysis frame is the optimal ZF precoder under total power constraint. Based on this analysis, a new precoder design is presented. The new design removes the minimum phase assumption of polyphase FB channel in the existing methods and gives rise to optimal noncausal (stable) precoder. It provides a general framework for optimal zero-forcing precoding under total power constraint. The numerical results show that the new design outperforms existing causal stable design.
The effects of illness beliefs and chemotherapy impact on quality of life in Japanese and Dutch patients with breast or lung cancer.

BACKGROUND Responses to diagnosis and treatment of cancer are mediated by a patient's illness perceptions. Such perceptions, though different among individuals, may be culturally dependent, and act upon health related quality of life (HRQOL). Over time, individual patients show different types of response trajectories. Four issues were investigated: (I) country and disease differences in illness beliefs between Japanese and Dutch patients with lung or breast cancer; (II) country and disease differences in HRQOL in early chemotherapy; (III) individual, country, and disease differences among HRQOL trajectories; (IV) the impact of illness beliefs on HRQOL trajectories. METHODS A total of 89 Japanese and Dutch patients with lung or breast cancer cooperated immediately before, one week after, and eight weeks after the start of chemotherapy. Data included the EORTC QLQ-C30 quality of life (QL) questionnaire and the Brief Illness Perception Questionnaire (B-IPQ). EORTC QLQ-C30 scales were summarized by two dimensions: generalized quality of life (GENQOL) and psychological well-being (PSYQOL). RESULTS (I) Japanese patients had higher means on B-IPQ's concern and time line than Dutch patients. Japanese lung cancer patients had a higher mean on treatment control than all other patients; (II) no differences between country and cancer type occurred on the two HRQOL dimensions. First assessment HRQOL differed significantly from the second and third assessments without differences between the latter two. Between the first two assessments, a decrease in GENQOL occurred, together with an improvement in PSYQOL; (III) individual differences dominated the trajectories; (IV) negative beliefs usually coincided with lower scores on GENQOL and PSYQOL. Patients initially lower on PSYQOL generally showed larger improvement. CONCLUSIONS Individual differences in HRQOL dominate differences between culture and cancer type, and illness beliefs influence HRQOL changes in individual patients. Clinical application is possible through influencing the patient's illness beliefs to create an optimal starting position for chemotherapy.
Population biology of a selfish sex ratio distorting element in a booklouse (Psocodea: Liposcelis)

Arthropods harbour a variety of selfish genetic elements that manipulate reproduction to be preferentially transmitted to future generations. A major ongoing question is to understand how these elements persist in nature. In this study, we examine the population dynamics of an unusual selfish sex ratio distorter in a recently discovered species of booklouse, Liposcelis sp. (Psocodea: Liposcelididae) to gain a better understanding of some of the factors that may affect the persistence of this element. Females that carry the selfish genetic element only ever produce daughters, although they are obligately sexual. These females also only transmit the maternal half of their genome. We performed a replicated population cage experiment, varying the initial frequency of females that harbour the selfish element, and following female frequencies for 20 months. The selfish genetic element persisted in all cages, often reaching very high (and thus severely female‐biased) frequencies. Surprisingly, we also found that females that carry the selfish genetic element had much lower fitness than their nondistorter counterparts, with lower lifetime fecundity, slower development and a shorter egg‐laying period. We suggest that differential fitness plays a role in the maintenance of the selfish genetic element in this species. We believe that the genetic system in this species, paternal genome elimination, which allows maternal control of offspring sex ratio, may also be important in the persistence of the selfish genetic element, highlighting the need to consider species with diverse ecologies and genetic systems when investigating the effects of sex ratio manipulators on host populations.
LR-AKE-Based AAA for Network Mobility (NEMO) Over Wireless Links

Network mobility introduces far more complexity than host mobility. Therefore, host mobility protocols such as Mobile IPv6 (MIPv6) need to be extended to support this new type of mobility. To address the extensions needed for network mobility, the IETF NEMO working group has recently standardized the network mobility basic support protocol in RFC 3963. However, in this RFC, it is not mentioned how authentication authorization and accounting (AAA) issues are handled in NEMO environment. Also, the use of IPsec to secure NEMO procedures does not provide robustness against leakage of stored secrets. To address this security issue and to achieve AAA with mobility, we propose new handover procedures to be performed by mobile routers and by visiting mobile nodes. This new handover procedure is based on leakage resilient-authenticated key establishment (LR-AKE) protocol. Using analytical models, we evaluate the proposed handover procedure in terms of handover delay which affects the session continuity. Our performance evaluation is based on transmission, queueing and encryption delays over wireless links
Methods, transparency and reporting of clinical trials in orthodontics and periodontics

Objective: The aim of this study was to explore the methods, reporting and transparency of clinical trials in orthodontics and compare them to the field of periodontics, as a standard within dentistry. Design/setting: Cross-sectional bibliographic study Methods: A total of 300 trials published in 2017–2018 and evenly distributed in orthodontics and periodontics were selected, assessed and analysed statistically to explore key aspects of the conduct and reporting of orthodontic clinical trials compared to trials in periodontics. Results: Several aspects are often neglected in orthodontic and periodontic trials and could be improved upon, including use of statistical expertise (22.3% of assessed trials), blinding of outcome assessors (62.3%), prospective trial registration (12.0%), adequate sample size calculation (35.7%), adherence to CONSORT (14.3%) and open data sharing (4.3%). The prevalence of statistically significant findings among orthodontic and periodontic trials was 62.3%, which was significantly associated with several methodological traits like statistician involvement (odds ratio [OR] = 0.5; 95% confidence interval [CI] = 0.3–0.9), blind outcome assessor (OR = 0.5; 95% CI = 0.2–1.0), lack of prospective trial registration (OR = 2.8; 95% CI = 1.3–5.9) and non-adherence to CONSORT (OR = 4.5; 95% CI = 1.3–15.8). Conclusions: Although trials in orthodontics seem to be significantly worse compared to periodontics in aspects like trial registration, adherence to CONSORT and declaration of competing interests or financial support, their methods do seem to have improved considerably in recent years.
Cis- and trans-acting variants contribute to survivorship in a naïve Drosophila melanogaster population exposed to ryanoid insecticides

Significance Around the world insecticides are being deregistered and banned, as their environmental costs are deemed too great or their efficacy against pest insects is reduced through the evolution of insecticide resistance. With the introduction of replacement insecticides comes the responsibility to assess the way new insecticides perturb various levels of biological systems, from insect physiology to ecosystems. We used a systems genetics approach to identify genetic variants affecting survivorship of Drosophila melanogaster exposed to chlorantraniliprole. The study population was completely naïve to this insecticide chemistry and yet we find associations with variants in neuromuscular genes and coregulated detoxification genes. We predict that these variants will increase in populations of this “sentinel species” as these insecticides are applied in the environment. Insecticide resistance is a paradigm of microevolution, and insecticides are responsible for the strongest cases of recent selection in the genome of Drosophila melanogaster. Here we use a naïve population and a novel insecticide class to examine the ab initio genetic architecture of a potential selective response. Genome-wide association studies (GWAS) of chlorantraniliprole susceptibility reveal variation in a gene of major effect, Stretchin Myosin light chain kinase (Strn-Mlck), which we validate with linkage mapping and transgenic manipulation of gene expression. We propose that allelic variation in Strn-Mlck alters sensitivity to the calcium depletion attributable to chlorantraniliprole’s mode of action. GWAS also reveal a network of genes involved in neuromuscular biology. In contrast, phenotype to transcriptome associations identify differences in constitutive levels of multiple transcripts regulated by cnc, the homolog of mammalian Nrf2. This suggests that genetic variation acts in trans to regulate multiple metabolic enzymes in this pathway. The most outstanding association is with the transcription level of Cyp12d1 which is also affected in cis by copy number variation. Transgenic overexpression of Cyp12d1 reduces susceptibility to both chlorantraniliprole and the closely related insecticide cyantraniliprole. This systems genetics study reveals multiple allelic variants segregating at intermediate frequency in a population that is completely naïve to this new insecticide chemistry and it foreshadows a selective response among natural populations to these chemicals.
Social Inequity and Structural Barriers to Completion of Ecological Momentary Assessments for Young Men Who Have Sex With Men and Trans Women Living With HIV in San Francisco

Background Ecological momentary assessments (EMAs) administered via text messaging facilitate real-time data collection. With widespread cell phone access, EMAs are becoming more available to even the most disenfranchised communities, such as those living with HIV. However, structural barriers disproportionately burden young men who have sex with men (MSM) and trans women (TW) living with HIV and threaten participation in HIV research. Objective We aim to identify structural barriers to completing EMA text surveys nested within a digital HIV care intervention for young MSM and TW living with HIV in San Francisco. Methods A total of 10,800 EMA text messages were delivered daily over 90 days to 120 participants enrolled in the Health eNav intervention (2017-2018) at the San Francisco Department of Public Health. EMA surveys inquired about participants’ daily affect, sexual behaviors, substance use, and treatment adherence. Survey completion was calculated after 30, 60, and 90 days of follow-up. We described characteristics of nonstarters (those who provided less than four complete responses to the first seven EMA surveys) and analyzed structural correlates of days to first weeklong or more EMA survey noncompletion using multivariable Cox proportional hazards regression. Qualitative interviews were used to evaluate the acceptability of EMA surveys. Results Participants completed 4384 of 10,800 (40.59%) EMA surveys. Completion of 70% or more of EMA surveys was attained by 56 of 120 participants (46.7%) at 30 days of follow-up, 40/120 (33.3%) at 60 days of follow-up, and 30/120 (25.0%) by the end of the 90-day study period. Twenty-eight participants (23.3%) were identified as nonstarters, and were more likely to be recently incarcerated (prevalence ratio [PR] 2.3, 95% CI 1.3-4.4), forego basic needs for HIV medications (PR 2.4, 95% CI 1.3-4.5), and be diagnosed with HIV in the last year (PR 2.2, 95% CI 1.1-4.1). Adjusting for nonstarters, young MSM and TW living in temporary/transitional housing (adjusted hazard ratio [aHR] 1.8, 95% CI 1.1-3.0), foregoing HIV medications to afford basic needs (aHR 1.7, 95% CI 1.1-2.7), and having less than a college education (aHR 3.5, 95% CI 1.4-9.0) had greater hazard of weeklong or more EMA survey noncompletion. Overall, there was high acceptability of the EMA surveys. Conclusions Although access to and use of technology is increasingly ubiquitous, this analysis demonstrates persisting gaps in EMA completion by socioeconomic factors such as incarceration, education level, housing, and competing needs for young MSM and TW living with HIV in San Francisco. Moreover, those recently diagnosed with HIV were more likely to experience an immediate drop-off in completing EMA surveys. EMAs are feasible for individuals not experiencing social inequity and structural barriers. HIV prevention technologies addressing these barriers and leveraging similar methodology may prove effective for young MSM and TW living with HIV.
A Data- and Workload-Aware Query Answering Algorithm for Range Queries Under Differential Privacy

We describe a new algorithm for answering a given set of range queries under e-differential privacy which often achieves substantially lower error than competing methods. Our algorithm satisfies differential privacy by adding noise that is adapted to the input data and to the given query set. We first privately learn a partitioning of the domain into buckets that suit the input data well. Then we privately estimate counts for each bucket, doing so in a manner well-suited for the given query set. Since the performance of the algorithm depends on the input database, we evaluate it on a wide range of real datasets, showing that we can achieve the benefits of data-dependence on both "easy" and "hard" databases.
Treatment of chronic HCV infection with DAAs in Rio de Janeiro/Brazil: SVR rates and baseline resistance analyses in NS5A and NS5B genes

The selection of viral strains with resistance-associated substitutions at hepatitis C virus (HCV) NS5A and NS5B genes is considered one of the limiting factors for achieving sustained virologic response (SVR) to combination of direct-acting antivirals daclatasvir (DCV) and sofosbuvir (SOF). Since 2015, this interferon-free regimen has been available in Brazilian clinical routine for treating mono- and HCV/HIV-coinfected patients chronically infected with genotypes 1 and 3. Our aim was to assess SVR rate for Brazilian patients chronically infected with genotypes 1 and 3 after DCV/SOF therapy and the frequency of baseline RASs in HCV NS5A and NS5B genes. Serum samples were collected from 107 monoinfected patients and 25 HCV/HIV co-infected patients before antiviral therapy with DCV/SOF. Genetic diversity of NS5A and NS5B genes was assessed by direct nucleotide sequencing. Overall, SVR rate was 95.4% (126/132), and treatment failure occurred in five monoinfected and one HCV/HIV co-infected patient. NS5A RASs frequency was higher for HCV/HIV patients (28%) than monoinfected patients (16.8%). No difference was evidenced between mono- and HCV/HIV-coinfected groups (15% vs. 16%) regarding NS5B gene. Genotype (GT) 1b strains had significantly more baseline substitutions in NS5A (31.6%) than GT 1a and 3a. At least one primary NS5A RAS described in literature at loci 28, 30, 31 or 93 was identified in HCV GTs 1 strains for both groups. As for NS5B, RASs at positions 159 and 316 was observed only in GT 1b strains. This study highlighted that SVR rate in clinical routine in Brazil was similar to randomized clinical trials (89–98%). Our research provided genetic data about the circulation of resistant variants in Brazil. Despite its presence, most of identified baseline mutations did not negatively impact treatment outcome. Genetic diversity of circulating strains suggested that most of the Brazilian HCV chronic carriers are susceptible to new therapeutic regimens including recently approved DAAs.
Decision tree fields

This paper introduces a new formulation for discrete image labeling tasks, the Decision Tree Field (DTF), that combines and generalizes random forests and conditional random fields (CRF) which have been widely used in computer vision. In a typical CRF model the unary potentials are derived from sophisticated random forest or boosting based classifiers, however, the pairwise potentials are assumed to (1) have a simple parametric form with a pre-specified and fixed dependence on the image data, and (2) to be defined on the basis of a small and fixed neighborhood. In contrast, in DTF, local interactions between multiple variables are determined by means of decision trees evaluated on the image data, allowing the interactions to be adapted to the image content. This results in powerful graphical models which are able to represent complex label structure. Our key technical contribution is to show that the DTF model can be trained efficiently and jointly using a convex approximate likelihood function, enabling us to learn over a million free model parameters. We show experimentally that for applications which have a rich and complex label structure, our model achieves excellent results.
Predicting human disease mutations and identifying drug targets from mouse gene knockout phenotyping campaigns

ABSTRACT Two large-scale mouse gene knockout phenotyping campaigns have provided extensive data on the functions of thousands of mammalian genes. The ongoing International Mouse Phenotyping Consortium (IMPC), with the goal of examining all ∼20,000 mouse genes, has examined 5115 genes since 2011, and phenotypic data from several analyses are available on the IMPC website (www.mousephenotype.org). Mutant mice having at least one human genetic disease-associated phenotype are available for 185 IMPC genes. Lexicon Pharmaceuticals' Genome5000™ campaign performed similar analyses between 2000 and the end of 2008 focusing on the druggable genome, including enzymes, receptors, transporters, channels and secreted proteins. Mutants (4654 genes, with 3762 viable adult homozygous lines) with therapeutically interesting phenotypes were studied extensively. Importantly, phenotypes for 29 Lexicon mouse gene knockouts were published prior to observations of similar phenotypes resulting from homologous mutations in human genetic disorders. Knockout mouse phenotypes for an additional 30 genes mimicked previously published human genetic disorders. Several of these models have helped develop effective treatments for human diseases. For example, studying Tph1 knockout mice (lacking peripheral serotonin) aided the development of telotristat ethyl, an approved treatment for carcinoid syndrome. Sglt1 (also known as Slc5a1) and Sglt2 (also known as Slc5a2) knockout mice were employed to develop sotagliflozin, a dual SGLT1/SGLT2 inhibitor having success in clinical trials for diabetes. Clinical trials evaluating inhibitors of AAK1 (neuropathic pain) and SGLT1 (diabetes) are underway. The research community can take advantage of these unbiased analyses of gene function in mice, including the minimally studied ‘ignorome’ genes. Summary: Large-scale, focused phenotyping campaigns provide data for thousands of mutant mouse genes, yielding key information for understanding rare human diseases and for developing novel drug therapies.
Individual and social stress, social capital, and depressive symptoms as predictors of adolescent suicide in South Korea: A mediated moderation model

This study examined the interactive effects of strain induced by individual and social stress and social capital on suicide, highlighting depressive symptoms as mediator in these relationships. This study used data from 5000 adolescents aged 14–18 years. Strain due to individual stress was found to have a direct effect on suicide, but strain due to social stress did not have a direct effect on suicide. The interactive effect of strain and social capital significantly predicted depressive symptoms and suicide. In the relationship between strain and suicide, the interactive effect of strain and social capital was mediated by depressive symptoms.