Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting compositionality to explore a large space of model structures

The recent proliferation of richly structured probabilistic models raises the question of how to automatically determine an appropriate model for a dataset. We investigate this question for a space of matrix decomposition models which can express a variety of widely used models from unsupervised learning. To enable model selection, we organize these models into a context-free grammar which generates a wide variety of structures through the compositional application of a few simple rules. We use our grammar to generically and efficiently infer latent components and estimate predictive likelihood for nearly 2500 structures using a small toolbox of reusable algorithms. Using a greedy search over our grammar, we automatically choose the decomposition structure from raw data by evaluating only a small fraction of all models. The proposed method typically finds the correct structure for synthetic data and backs off gracefully to simpler models under heavy noise. It learns sensible structures for datasets as diverse as image patches, motion capture, 20 Questions, and U.S. Senate votes, all using exactly the same code.
Precise BER analysis of π/4-DQPSK OFDM with carrier frequency offset over frequency selective fast fading channels

An exact closed-form bit error rate (BER) expression is derived for an orthogonal frequency-division multiplexing system with π/4-shifted differentially encoded quadrature phase shift keying (π/4-DQPSK) in the presence of carrier frequency offset over frequency-selective fast Rayleigh fading channels. Different system configurations, including time domain differential modulation, frequency domain differential modulation, single channel reception, and multi-channel reception with maximal ratio combining diversity, are considered in the exact BER analysis. For a small number of subcarriers, the BER expression can be calculated directly. A Monte Carlo method is designed to evaluate the BER for a large number of subcarriers. The analytical expression can be used to investigate the effect of several channel parameters, including mean delay spread and maximum Doppler spread, on the system BER performance. Particularly, the effect of carrier frequency offset on the system performance, and the differences and opportunities to use frequency domain differential modulation or time domain differential modulation, can be studied in a quantitative way for a more realistic wireless channel environment model. By using the exact closed-form BER expression, an optimum number of subcarriers can be found, and the allowable carrier frequency offset, Doppler spread, and mean delay spread for given operating conditions can be determined.
Vector-Isovector Excitations at Finite Density and Temperature and the Validity of Brown-Rho Scaling

Recent work reported at the Quark Matter Conference 2005 has led to the suggestion that Brown-Rho scaling is ruled out by the NA60 data. (Brown-Rho scaling describes the reduction of hadronic masses in matter and at finite temperature.) In the present work we argue that the interpretation of the experimental data presented at the Quark Matter Conference is not correct and that Brown-Rho scaling is valid. To make this argument we discuss the evolution in time of the excited hadronic system and suggest that the system is deconfined at the earliest times and becomes confined when the density and temperature decrease as the system evolves. Thus, we suggest that we see both the properties of the deconfined and confined systems in the experimental data. In our interpretation, Brown-Rho scaling refers to the later times of the collision, when the system is in the confined phase.
A genome-wide screen for identifying all regulators of a target gene

We have developed a new screening methodology for identifying all genes that control the expression of a target gene through genetic or metabolic interactions. The screen combines mutant libraries with luciferase reporter constructs, whose expression can be monitored in vivo and over time in different environmental conditions. We apply the method to identify the genes that control the expression of the gene acs, encoding the acetyl coenzyme A synthetase, in Escherichia coli. We confirm most of the known genetic regulators, including CRP–cAMP, IHF and components of the phosphotransferase system. In addition, we identify new regulatory interactions, many of which involve metabolic intermediates or metabolic sensing, such as the genes pgi, pfkA, sucB and lpdA, encoding enzymes in glycolysis and the TCA cycle. Some of these novel interactions were validated by quantitative reverse transcriptase-polymerase chain reaction. More generally, we observe that a large number of mutants directly or indirectly influence acs expression, an effect confirmed for a second promoter, sdhC. The method is applicable to any promoter fused to a luminescent reporter gene in combination with a deletion mutant library.
Cognition and Mood-Related Behaviors in L3mbtl1 Null Mutant Mice

Alterations in histone lysine methylation and epigenetic regulators of gene expression could play a role in the neurobiology and treatment of patients diagnosed with mood spectrum disorder, including depression and anxiety. Mutations and altered expression of various lysine methyltransferases (KMTs) and demethylases (KDMs) have been linked to changes in motivational and emotional behaviors in preclinical model systems. However, it is not known whether regulators operating downstream of histone lysine methylation could affect mood-related behavior. Malignant Brain Tumor (MBT) domain ‘chromatin reader’ proteins bind to methylated histone lysine residues and associate with chromatin remodeling complexes to facilitate or repress gene expression. MBT proteins, including the founding member, L3mbtl1, maintain high levels of expression in neurons of the mature brain. Here, we exposed L3mbtl1 null mutant mice to a wide range of tests exploring cognition and mood-relevant behaviors at baseline and in the context of social isolation, as a stressor to elicit depression-related behavior in susceptible mice. L3mbtl1 loss-of-function was associated with significant decreases in depression and and anxiety in some of the behavioral paradigms. This was not associated with a more generalized neurological dysfunction because cognition and memory remained unaltered in comparison to controls. These findings warrant further investigations on the role of MBT chromatin reader proteins in the context of emotional and affective behaviors.
Incrementally parallelizing database transactions with thread-level speculation

With the advent of chip multiprocessors, exploiting intratransaction parallelism in database systems is an attractive way of improving transaction performance. However, exploiting intratransaction parallelism is difficult for two reasons: first, significant changes are required to avoid races or conflicts within the DBMS; and second, adding threads to transactions requires a high level of sophistication from transaction programmers. In this article we show how dividing a transaction into speculative threads solves both problems—it minimizes the changes required to the DBMS, and the details of parallelization are hidden from the transaction programmer. Our technique requires a limited number of small, localized changes to a subset of the low-level data structures in the DBMS. Through this method of incrementally parallelizing transactions, we can dramatically improve performance: on a simulated four-processor chip-multiprocessor, we improve the response time by 44--66% for three of the five TPC-C transactions, assuming the availability of idle processors.
Variational Dual-Tree Framework for Large-Scale Transition Matrix Approximation

In recent years, non-parametric methods utilizing random walks on graphs have been used to solve a wide range of machine learning problems, but in their simplest form they do not scale well due to the quadratic complexity. In this paper, a new dual-tree based variational approach for approximating the transition matrix and efficiently performing the random walk is proposed. The approach exploits a connection between kernel density estimation, mixture modeling, and random walk on graphs in an optimization of the transition matrix for the data graph that ties together edge transitions probabilities that are similar. Compared to the de facto standard approximation method based on k-nearest-neighbors, we demonstrate order of magnitudes speedup without sacrificing accuracy for Label Propagation tasks on benchmark data sets in semi-supervised learning.
Psychosocial Factors and Risk of Incident Heart Failure: The Multi-Ethnic Study of Atherosclerosis.

BACKGROUND Heart failure (HF) is a major source of morbidity and mortality in the United States. Psychosocial factors have frequently been studied as risk factors for coronary heart disease but not for HF. METHODS AND RESULTS We examined the relationship between psychological status and incident HF among 6782 individuals from the Multi-Ethnic Study of Atherosclerosis (MESA). Anger, anxiety, chronic stress, depressive symptoms, and hostility were measured using validated scales, and physician reviewers adjudicated incident HF events. Cox proportional hazards models were used to adjust for relevant demographic, behavioral, and physiological covariates. Interactions by age, race, sex, and self-reported health were examined in exploratory analyses. During a mean follow-up of 9.3 years, 242 participants developed incident HF. There was no association between psychosocial factors and HF hazard ratios (95% confidence interval) for the highest versus lowest quartile: anger=1.14 (0.81-1.60), anxiety=0.74 (0.51-1.07), chronic stress=1.25 (0.90-1.72), depressive symptoms=1.19 (0.76-1.85), and hostility=0.95 (0.62-1.42). In exploratory analysis, among the participants reporting fair/poor health at baseline, those reporting high versus low levels of anxiety, chronic stress, and depressive symptoms had 2-fold higher risk of incident HF, but there was no association for those with good/very good/excellent self-reported health. CONCLUSIONS Overall, these psychosocial factors were not significantly associated with incident HF. However, for participants reporting poor health at baseline, there was evidence that anxiety, chronic stress, and depressive symptoms were associated with increased risk of HF. Future research with greater statistical power is necessary to replicate these findings and seek explanations.
Differential expression of sirtuins in the aging rat brain

Although there are seven mammalian sirtuins (SIRT1-7), little is known about their expression in the aging brain. To characterize the change(s) in mRNA and protein expression of SIRT1-7 and their associated proteins in the brain of “physiologically” aged Wistar rats. We tested mRNA and protein expression levels of rat SIRT1-7, and the levels of associated proteins in the brain using RT-PCR and western blotting. Our data shows that SIRT1 expression increases with age, concurrently with increased acetylated p53 levels in all brain regions investigated. SIRT2 and FOXO3a protein levels increased only in the occipital lobe. SIRT3-5 expression declined significantly in the hippocampus and frontal lobe, associated with increases in superoxide and fatty acid oxidation levels, and acetylated CPS-1 protein expression, and a reduction in MnSOD level. While SIRT6 expression declines significantly with age acetylated H3K9 protein expression is increased throughout the brain. SIRT7 and Pol I protein expression increased in the frontal lobe. This study identifies previously unknown roles for sirtuins in regulating cellular homeostasis and healthy aging.
Pain management in the acute care setting: Update and debates

Pain management in the paediatric acute care setting is underutilised and can be improved. An awareness of the analgesic options available and their limitations is an important starting point. This article describes the evolving understanding of relevant pharmacogenomics and safety data of the various analgesic agents with a focus on agents available in Australia and New Zealand. It highlights the concerns with the use of codeine in children and discusses alternative oral opioids. Key features of oral, parenteral, inhaled and intranasal analgesic agents are discussed, as well as evidence supported use of sweet tasting solutions and non‐pharmacological interventions. One of the biggest changes in acute care pain management has been the advent of intranasal fentanyl providing reliable potent analgesia without the need for intravenous access. The article will also address the issue of multimodal analgesia where a single agent is insufficient.
Nutritional and Phenolic Composition of Morinda Citrifolia L. (Noni) Fruit at Different Ripeness Stages and Seasonal Patterns Harvested in Nayarit, Mexico

Morinda citrifolia L. (Noni) fruit harvested in Tepic, Nayarit, Mexico presented alterations in its composition and its properties with the process of senescence during ripening and the seasons of harvest. Various stages of maturity (stages 1- 4) were examined for their physico-chemical properties (moisture, soluble protein, total carbohydrates, titratable acidity, pH, soluble solids, ash, vitamin C, and phenolic compounds). Generally maturation increased moisture, soluble protein, total carbohydrates, total acidity, vitamin C, and phenolic compounds. During May-June noni fruits (stages 1-4) had the highest levels of soluble protein (8.73-15.63 g/100 g FW), total carbohydrates (6.60-9.60 g/100g FW), ash (0.87-1.34 g/100 g FW), ascorbic acid (115.85-182.42 mg/100 g FW) and total phenols (3022.8-3647.0 μg/g FW). Middle stage (stage 2) and ripe soft noni fruits (stage 4) had greater total phenolic and rutin (47.18-69.88 μg/g FW-stage 2 and 65.22-81.34 μg/g FW-stage 4); this profile appears to be independent of season.
A hybrid codebook background model for background subtraction

Real-time segmentation of scene into foreground and background is an important issue for many applications. Different from previous codebook (CB) methods, this paper introduces a hybrid CB model by combining the mixture of Gaussian (MOG) method and the CB method. It can be used to solve the problems of moving background and shadow/highlight on the background and background. Our method avoids extracting false foreground pixels or missing real foreground pixels. The experimental results illustrate the advantages of our method over the other methods.
Performance Trade-Offs of a IEEE 802.21-Based Vertical Handover Decision Algorithm under Different Network Conditions

Wireless technologies have been widely deployed in the last decade making users demand for continuous connectivity. Users not only demand being attached to a network, but possibly to the one with the highest performance, or at least to a network able to fulfill their requirements. To choose the best network among different candidates, the IEEE 802.21 standard has been developed. In this paper we aim at demonstrating the viability of performing Vertical Handover (VHO) processes based on the IEEE 802.21 protocol. To do so, we have evaluated a VHO strategy which considers network availability and maximum data rate in order to choose the best network candidate among the Wi-Fi, the WiMAX, and the UMTS. Moreover, throughout a set of experiments, we have also evaluated the maximum performance of the available networks.
The pro-domains of neurotrophins, including BDNF, are linked to Alzheimer's disease through a toxic synergy with Aβ

Brain-derived neurotrophic factor (BDNF) has a crucial role in learning and memory by promoting neuronal survival and modulating synaptic connectivity. BDNF levels are lower in the brains of individuals with Alzheimer's disease (AD), suggesting a pathogenic involvement. The Drosophila orthologue of BDNF is the highly conserved Neurotrophin 1 (DNT1). BDNF and DNT1 have the same overall protein structure and can be cleaved, resulting in the conversion of a full-length polypeptide into separate pro- and mature-domains. While the BDNF mature-domain is neuroprotective, the role of the pro-domain is less clear. In flies and mammalian cells, we have identified a synergistic toxic interaction between the amyloid-β peptide (Aβ1–42) and the pro-domains of both DNT1 and BDNF. Specifically, we show that DNT1 pro-domain acquires a neurotoxic activity in the presence of Aβ1–42. In contrast, DNT1 mature-domain is protective against Aβ1–42 toxicity. Likewise, in SH-SY5Y cell culture, BDNF pro-domain is toxic only in the presence of Aβ1–42. Western blots indicate that this synergistic interaction likely results from the Aβ1–42-induced upregulation of the BDNF pro-domain receptor p75NTR. The clinical relevance of these findings is underlined by a greater than thirty fold increase in the ratio of BDNF pro- to mature-domains in the brains of individuals with AD. This unbalanced BDNF pro:mature-domain ratio in patients represents a possible biomarker of AD and may offer a target for therapeutic intervention.
Pneumonia diagnosis in childhood and incidence of leukaemia, lymphoma and brain cancer: a Danish nationwide cohort study

Objectives There is an ongoing debate on the possible association between infections in early childhood and subsequent cancer risk, but it remains unclear if a hospital admission for infection is associated with risk of childhood cancer diagnosis. We examined if a hospital-based diagnosis of pneumonia was a clinical marker of the three most common childhood cancers. Design Population-based cohort study. Setting Denmark, hospital diagnoses, 1994–2013. Methods Using national health registries, we compared the observed incidence of leukaemia, lymphoma and brain cancer among 83 935 children with a hospital-based pneumonia diagnosis with that expected among children in the general population. We calculated absolute cancer risks and standardised incidence ratios (SIRs) as a measure of relative risk. Results The cancer SIRs were substantially increased during the first 6 months of follow-up; lymphoid leukaemia: 6.2 (95% CI 3.5 to 10.3); myeloid leukaemia: 14.8 (95% CI 6.0 to 30.6); Hodgkin’s lymphoma: 60.8 (95% CI 26.2 to 120), non-Hodgkin’s lymphoma: 15.9 (95% CI 5.2 to 37.2) and brain cancer: 4.4 (95% CI 1.9 to 8.7). The 6-month absolute risks of leukaemia, lymphoma and brain cancer were all low, reaching 0.05% when combined. An increased risk persisted beyond 5 years for non-Hodgkin’s lymphoma and brain cancer. However, the 5-year absolute cancer risk was 0.14%. Conclusions The short-term incidence of leukaemia, lymphoma and brain cancer was higher than expected and persisted beyond 5 years for non-Hodgkin’s lymphoma and brain cancer. However, the absolute cancer risk was low.
Cooperative and independent activities of Sgt2 and Get5 in the targeting of tail-anchored proteins

Abstract TPR proteins modulate the activity of molecular chaperones. Here, we describe the S. cerevisiae TPR protein Sgt2 as interaction partner of Ssa1 and Hsp104 and as a component of the GET pathway by interacting with Get5. The GET pathway mediates the sorting of tail-anchored (TA) proteins, harboring a C-terminal trans-membrane segment, to the ER membrane. S. cerevisiae sgt2Δ cells show partial defects in TA protein sorting. Sgt2 activity in vivo relies on its N- and C-terminal domains, whereas the central TPR domain and thus chaperone interactions are dispensable. We show that TA protein sorting defects are more severe in sgt2Δ get5Δ mutants compared to single knockouts. Furthermore, overproduction of Sgt2 becomes toxic to get3Δ but not to get5Δ cells. Together, these findings indicate an additional, Get5-independent role of Sgt2 in TA protein sorting, pointing to parallel pathways of substrate delivery to Get3.
Multilevel Modeling Analysis of Odontogenic Risk Factors and Nasal Septum Deviation Associated with Maxillary Sinus Mucosal Thickening: A Cone-Beam Computed Tomography Study

(1) Background: In this study, the impact of odontogenic risk factors with nasal septum deviation on maxillary sinus mucosal thickening was assessed using Cone-beam computed tomography CBCT. (2) Methods: A total of 328 maxillary sinus regions from 164 patients (85 males and 79 females) were examined. Images were interpreted by dental specialists and Otolaryngologists. Coronal and sagittal sections were examined to assess the proximity of the root tips of posterior maxillary teeth (RPMT) to the maxillary sinus. The periodontal bone loss for all maxillary posterior teeth was also assessed. Consequently, maxillary sinus mucosal thickening (MT) was further classified into three gradings. Multilevel modeling regression analysis was used due to the hierarchical structuring of the data. Four models were developed, a null model with no factors, a model with tooth-level factors (RPMT, PBL, tooth condition, and root length), a model with patient-level factors (gender and nasal septum deviation), and a model with combined patient- and tooth-level factors. Regression estimates (AOR) and 95% confidence intervals (CIs) of individual and tooth factors were calculated. (3) Results: Multilevel regression analysis showed that RPMT was significantly associated with MT of maxillary sinus (p < 0.001), where patients who had RPMT > 0 had higher odds of MT of maxillary sinus. Tooth condition was also found to be significantly associated with MT of maxillary sinus, where teeth with failed RCT (p < 0.001) and teeth with restorations (p < 0.008) had higher odds of MT of maxillary sinus (AOR = 2.87, 95%CI 1.65, 4.42, AOR = 1.64, 95%CI 1.14, 2.36, respectively). (4) Conclusions: In order to plan preoperative treatment for maxillary posterior teeth, it is important to assess the anatomical relationship between the sinus floor and the root tips of the maxillary posterior teeth. Additionally, we establish a better understanding of the clinician before surgical intervention is conducted.
Restoring Fertility in Sterile Childhood Cancer Survivors by Autotransplanting Spermatogonial Stem Cells: Are We There Yet?

Current cancer treatment regimens do not only target tumor cells, but can also have devastating effects on the spermatogonial stem cell pool, resulting in a lack of functional gametes and hence sterility. In adult men, fertility can be preserved prior to cancer treatment by cryopreservation of ejaculated or surgically retrieved spermatozoa, but this is not an option for prepubertal boys since spermatogenesis does not commence until puberty. Cryopreservation of a testicular biopsy taken before initiation of cancer treatment, followed by in vitro propagation of spermatogonial stem cells and subsequent autotransplantation of these stem cells after cancer treatment, has been suggested as a way to preserve and restore fertility in childhood cancer survivors. This strategy, known as spermatogonial stem cell transplantation, has been successful in mice and other model systems, but has not yet been applied in humans. Although recent progress has brought clinical application of spermatogonial stem cell autotransplantation in closer range, there are still a number of important issues to address. In this paper, we describe the state of the art of spermatogonial stem cell transplantation and outline the hurdles that need to be overcome before clinical implementation.