Miracle-dz/UniFAR-FTUs huggingface dataset:
SGD and Hogwild! Convergence Without the Bounded Gradients Assumption

Stochastic gradient descent (SGD) is the optimization algorithm of choice in many machine learning applications such as regularized empirical risk minimization and training deep neural networks. The classical convergence analysis of SGD is carried out under the assumption that the norm of the stochastic gradient is uniformly bounded. While this might hold for some loss functions, it is always violated for cases where the objective function is strongly convex. In (Bottou et al.,2016), a new analysis of convergence of SGD is performed under the assumption that stochastic gradients are bounded with respect to the true gradient norm. Here we show that for stochastic problems arising in machine learning such bound always holds; and we also propose an alternative convergence analysis of SGD with diminishing learning rate regime, which results in more relaxed conditions than those in (Bottou et al.,2016). We then move on the asynchronous parallel setting, and prove convergence of Hogwild! algorithm in the same regime, obtaining the first convergence results for this method in the case of diminished learning rate.
Some Results on the Independence Polynomial of Unicyclic Graphs

Abstract Let G be a simple graph on n vertices. An independent set in a graph is a set of pairwise non-adjacent vertices. The independence polynomial of G is the polynomial I(G,x)=∑k=0ns(G,k)xk $I(G,x) = \sum\nolimits_{k = 0}^n {s\left({G,k} \right)x^k }$ , where s(G, k) is the number of independent sets of G with size k and s(G, 0) = 1. A unicyclic graph is a graph containing exactly one cycle. Let Cn be the cycle on n vertices. In this paper we study the independence polynomial of unicyclic graphs. We show that among all connected unicyclic graphs G on n vertices (except two of them), I(G, t) > I(Cn, t) for sufficiently large t. Finally for every n ≥ 3 we find all connected graphs H such that I(H, x) = I(Cn, x).
RNF43 and ZNRF3 are commonly altered in serrated pathway colorectal tumorigenesis

Serrated pathway colorectal cancers (CRCs) are characterised by a BRAF mutation and half display microsatellite instability (MSI). The Wnt pathway is commonly upregulated in conventional CRC through APC mutation. By contrast, serrated cancers do not mutate APC. We investigated mutation of the ubiquitin ligases RNF43 and ZNRF3 as alternate mechanism of altering the Wnt signal in serrated colorectal neoplasia. RNF43 was mutated in 47/54(87%) BRAF mutant/MSI and 8/33(24%) BRAF mutant/microsatellite stable cancers compared to only 3/79(4%) BRAF wildtype cancers (p<0.0001). ZNRF3 was mutated in 16/54(30%) BRAF mutant/MSI and 5/33(15%) BRAF mutant/microsatellite stable compared to 0/27 BRAF wild type cancers (p=0.004). An RNF43 frameshift mutation (X659fs) occurred in 80% BRAF mutant/MSI cancers. This high rate was verified in a second series of 25/35(71%) BRAF mutant/MSI cancers. RNF43 and ZNRF3 had lower transcript expression in BRAF mutant compared to BRAF wildtype cancers and less cytoplasmic protein expression in BRAF mutant/MSI compared to other subtypes. Treatment with a porcupine inhibitor reduced RNF43/ZNRF3 mutant colony growth by 50% and synergised with a MEK inhibitor to dramatically reduce growth. This study suggests inactivation of RNF43 and ZNRF3 is important in serrated tumorigenesis and has identified a potential therapeutic strategy for this cancer subtype.
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell’s capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and bioengineering. It depends on enzyme parameters (such as kcat and KM constants), but also on metabolite concentrations. Moreover, similar amounts of different enzymes might incur different costs for the cell, depending on enzyme-specific properties such as protein size and half-life. Here, we developed enzyme cost minimization (ECM), a scalable method for computing enzyme amounts that support a given metabolic flux at a minimal protein cost. The complex interplay of enzyme and metabolite concentrations, e.g. through thermodynamic driving forces and enzyme saturation, would make it hard to solve this optimization problem directly. By treating enzyme cost as a function of metabolite levels, we formulated ECM as a numerically tractable, convex optimization problem. Its tiered approach allows for building models at different levels of detail, depending on the amount of available data. Validating our method with measured metabolite and protein levels in E. coli central metabolism, we found typical prediction fold errors of 4.1 and 2.6, respectively, for the two kinds of data. This result from the cost-optimized metabolic state is significantly better than randomly sampled metabolite profiles, supporting the hypothesis that enzyme cost is important for the fitness of E. coli. ECM can be used to predict enzyme levels and protein cost in natural and engineered pathways, and could be a valuable computational tool to assist metabolic engineering projects. Furthermore, it establishes a direct connection between protein cost and thermodynamics, and provides a physically plausible and computationally tractable way to include enzyme kinetics into constraint-based metabolic models, where kinetics have usually been ignored or oversimplified.
A putative LysR-type transcriptional regulator PrhO positively regulates the type III secretion system and contributes to the virulence of Ralstonia solanacearum.

LysR-type transcriptional regulators (LTTRs) are ubiquitous and abundant amongst bacteria and control a variety of cellular processes. Here, we investigated the effect of Rsc1880 (a putative LTTR, hereafter designated as PrhO) on the pathogenicity of Ralstonia solanacearum. Deletion of prhO substantially reduced the expression of the type III secretion system (T3SS) both in vitro and in planta, and resulted in significantly impaired virulence in tomato and tobacco plants. Complementary prhO completely restored the reduced virulence and T3SS expression to that of the wild-type. Moreover, PrhO-dependent T3SS and virulence were conserved amongst R. solanacearum species. However, deletion of prhO did not alter biofilm formation, swimming mobility and in planta growth. The expression of some type III effectors was significantly reduced in prhO mutants, but the hypersensitive response was not affected in tobacco leaves. Consistent with the key regulatory role of HrpB on T3SS, PrhO positively regulated the T3SS through HrpB. Furthermore, PrhO regulated hrpB expression via two close paralogues, HrpG and PrhG, which are two-component response regulators and positively regulate hrpB expression in a parallel manner. However, deletion of prhO did not alter the expression of phcA, prhJ and prhN, which are also involved in hrpB regulation. In addition, PrhO was expressed in a cell density-dependent manner, but negatively repressed by itself. No regulation was observed for HrpB, PhcA and PrhN on prhO expression. Taken together, we genetically demonstrated that PrhO is a novel virulence regulator of R. solanacearum, which positively regulates T3SS expression through HrpG, PrhG and HrpB and contributes to virulence.
Nutritional requirements of surgical and critically-ill patients: do we really know what they need?

Malnutrition remains a problem in surgical and critically-ill patients. In surgical patients the incidence of malnutrition ranges from 9 to 44%. Despite this variability there is a consensus that malnutrition worsens during hospital stay. In the intensive care unit (ICU), 43% of the patients are malnourished. Although poor nutrition during hospitalisation may be attributable to many factors, not least inadequacies in hospital catering services, there must also be the question of whether those patients who receive nutritional support are being fed appropriately. Indirect calorimetry is the ‘gold standard’ for determining an individual's energy requirements, but limited time and financial resources preclude the use of this method in everyday clinical practice. Studies in surgical and ICU patient populations have been reviewed to determine the ‘optimal’ energy and protein requirements of these patients. There are only a small number of studies that have attempted to measure energy requirements in the various surgical patient groups. Uncomplicated surgery has been associated with energy requirements of 1·0–1·15×BMR whilst complicated surgery requires 1·25–1·4×BMR in order to meet the patient's needs. Identifying the optimal requirements of ICU patients is far more difficult because of the heterogeneous nature of this population. In general, 5·6 kJ (25 kcal)/kg per d is an acceptable and achievable target intake, but patients with sepsis or trauma may require almost twice as much energy during the acute phase of their illness. The implications of failing to meet and exceeding the requirements of critically-ill patients are also reviewed.
The influence of presentation modality on the social comprehension of naturalistic scenes in adults with autism spectrum disorder

The comprehension of dynamically unfolding social situations is made possible by the seamless integration of multimodal information merged with rich intuitions about the thoughts and behaviors of others. We examined how high-functioning adults with autism spectrum disorder and neurotypical controls made a complex social judgment (i.e. rating the social awkwardness of scenes from a television sitcom) across three conditions that manipulated presentation modality—visual alone, transcribed text alone, or visual and auditory together. The autism spectrum disorder and control groups collectively assigned similar mean awkwardness ratings to individual scenes. However, individual participants with autism spectrum disorder tended to respond more idiosyncratically than controls, assigning ratings that were less correlated with the ratings of the other participants in the sample. We found no evidence that this group difference was isolated to any specific presentation modality. In a comparison condition, we found no group differences when participants instead rated the happiness of characters (a more basic social judgment) in full audiovisual format. Thus, although we observed differences in the manner with which high-functioning adults with autism spectrum disorder make social judgments compared to controls, these group differences may be dependent on the social dimension being judged, rather than the specific modality of presentation.
Facial Expression Recognition Based on Complexity Perception Classification Algorithm

Facial expression recognition (FER) has always been a challenging issue in computer vision. The different expressions of emotion and uncontrolled environmental factors lead to inconsistencies in the complexity of FER and variability of between expression categories, which is often overlooked in most facial expression recognition systems. In order to solve this problem effectively, we presented a simple and efficient CNN model to extract facial features, and proposed a complexity perception classification (CPC) algorithm for FER. The CPC algorithm divided the dataset into an easy classification sample subspace and a complex classification sample subspace by evaluating the complexity of facial features that are suitable for classification. The experimental results of our proposed algorithm on Fer2013 and CK-plus datasets demonstrated the algorithm's effectiveness and superiority over other state-of-the-art approaches.
Evidence of the differentiated structural arrangement of constitutive heterochromatin between two populations of Astyanax scabripinnis (Pisces, Characidae)

The composition of heterochromatin classes along the chromosomes of specimens from two populations of the fish Astyanax scabripinnis was examined using fluorescence banding with GC- and AT-DNA specific fluorochromes and fluorescence in situ hybridization (FISH) with an AT-rich satellite DNA (As51) probe. For the pericentromeric heterochromatin blocks neither GC/AT-DNA specific fluorochromes nor the FISH technique produce any response with chromosomes from either of the populations. On the other hand, the telomeric distal heterochromatin blocks of both populations fluoresced when the FISH technique was applied but showed distinct responses after GC-specific fluorochrome treatments, leading us to propose different structural arrangements of the FISH-positive heterochromatins. Such differences in chromosome banding patterns together with other karyotypic differences suggest differentiation of these populations at taxonomic level.
Correlates of self-harm and suicide attempts in justice-involved young people

The purpose of this study was to ascertain the prevalence and correlates of self-harm among young people in detention in Australia. The sample included 215 (177 male; 38 female) young people who were in youth detention in the state of Victoria, Australia. Participants were administered a series of questionnaires related to self-harm, mental health, socio-environmental experiences and behaviours. Overall, one-third (33%) of the sample reported previous self-harm and 12% reported at least one suicide attempt. In a multivariate logistic regression analysis, a history of childhood trauma, contact with mental health services, and low educational interest significantly increased the likelihood of self-harm. Young people who reported a suicide attempt scored significantly higher on the measure of childhood trauma than did youth who had engaged in non-suicidal self-harm. Findings demonstrate a strong connection between childhood traumatic experiences and suicidal behaviours for youth in detention. Trauma histories and mental health concerns must be considered when identifying youth at increased risk of self-harm.
MNK1/2 inhibition limits oncogenicity and metastasis of KIT-mutant melanoma

Melanoma can be stratified into unique subtypes based on distinct pathologies. The acral/mucosal melanoma subtype is characterized by aberrant and constitutive activation of the proto-oncogene receptor tyrosine kinase C-KIT, which drives tumorigenesis. Treatment of these melanoma patients with C-KIT inhibitors has proven challenging, prompting us to investigate the downstream effectors of the C-KIT receptor. We determined that C-KIT stimulates MAP kinase–interacting serine/threonine kinases 1 and 2 (MNK1/2), which phosphorylate eukaryotic translation initiation factor 4E (eIF4E) and render it oncogenic. Depletion of MNK1/2 in melanoma cells with oncogenic C-KIT inhibited cell migration and mRNA translation of the transcriptional repressor SNAI1 and the cell cycle gene CCNE1. This suggested that blocking MNK1/2 activity may inhibit tumor progression, at least in part, by blocking translation initiation of mRNAs encoding cell migration proteins. Moreover, we developed an MNK1/2 inhibitor (SEL201), and found that SEL201-treated KIT-mutant melanoma cells had lower oncogenicity and reduced metastatic ability. Clinically, tumors from melanoma patients harboring KIT mutations displayed a marked increase in MNK1 and phospho-eIF4E. Thus, our studies indicate that blocking MNK1/2 exerts potent antimelanoma effects and support blocking MNK1/2 as a potential strategy to treat patients positive for KIT mutations.
Association of the Timing of Pregnancy With Survival in Women With Breast Cancer

Importance Increasing numbers of women experience pregnancy around the time of, or after, a diagnosis of breast cancer. Understanding the effect of pregnancy on survival in women with breast cancer will help in the counseling and treatment of these women. Objective To compare the overall survival of women diagnosed with breast cancer during pregnancy or in the postpartum period with that of women who had breast cancer but did not become pregnant. Design, Setting, and Participants This population-based, retrospective cohort study linked health administrative databases in Ontario, Canada, comprising 7553 women aged 20 to 45 years at the time of diagnosis with invasive breast cancer, from January 1, 2003, to December 31, 2014. Exposures Any pregnancy in the period from 5 years before, until 5 years after, the index date of the diagnosis of breast cancer. Women were classified into the following 4 exposure groups: no pregnancy (the referent), pregnancy before breast cancer, pregnancy-associated breast cancer, and pregnancy following breast cancer. Main Outcomes and Measures Five-year actuarial survival rates for all exposure groups, age-adjusted and multivariable hazard ratios [HRs] of pregnancy for overall survival for all exposure groups, and time-dependent hazard ratios for women with pregnancy following breast cancer. Results Among the 7553 women in the study (mean age at diagnosis, 39.1 years; median, 40 years; range, 20-44 years) the 5-year actuarial survival rate was 87.5% (95% CI, 86.5%-88.4%) for women with no pregnancy, 85.3% (95% CI, 82.8%-87.8%) for women with pregnancy before breast cancer (age-adjusted hazard ratio, 1.03; 95% CI, 0.85-1.27; P = .73), and 82.1% (95% CI, 78.3%-85.9%) for women with pregnancy-associated breast cancer (age-adjusted hazard ratio, 1.18; 95% CI, 0.91-1.53; P = .20). The 5-year actuarial survival rate was 96.7% (95% CI, 94.1%-99.3%) for women who had pregnancy 6 months or more after diagnosis of breast cancer, vs 87.5% (95% CI, 86.5%-88.4%) for women with no pregnancy) (age-adjusted HR, 0.22; 95% CI, 0.10-0.49; P < .001). Conclusions and Relevance Pregnancy did not adversely affect survival in women with breast cancer. For breast cancer survivors who wish to conceive, the risk of death is lowest if pregnancy occurs 6 months or more after diagnosis.
Reshaping of Gait Coordination by Robotic Intervention in Myelopathy Patients After Surgery

The Ossification of the Posterior Longitudinal Ligament (OPLL) is an idiopathic degenerative spinal disease which may cause motor deficit. For patients presenting myelopathy or severe stenosis, surgical decompression is the treatment of choice; however, despite adequate decompression residual motor impairment is found in some cases. After surgery, there is no therapeutic approach available for this population. The Hybrid Assistive Limb® (HAL) robot suit is a unique powered exoskeleton designed to predict, support, and enhance the lower extremities performance of patients using their own bioelectric signals. This approach has been used for spinal cord injury and stroke patients where the walking performance improved. However, there is no available data about gait kinematics evaluation after HAL therapy. Here we analyze the effect of HAL therapy in OPLL patients in acute and chronic stages after decompression surgery. We found that HAL therapy improved the walking performance for both groups. Interestingly, kinematics evaluation by the analysis of the elevation angles of the thigh, shank, and foot by using a principal component analysis showed that planar covariation, plane orientation, and movement range evaluation improved for acute patients suggesting an improvement in gait coordination. Being the first study performing kinematics analysis after HAL therapy, our results suggest that HAL improved the gait coordination of acute patients by supporting the relearning process and therefore reshaping their gait pattern.
Experimental investigation of gas explosion characteristic in linked vessels

Many injuries and financial loss are usually caused by gas explosion in linked vessels when the vessels and pipes cannot bear high pressure and high rate of pressure rise.The high pressure and rate of pressure rise are mainly related with the characteristic of gas explosion in linked vessels.In order to obtain the rule and characteristic of gas explosion in linked vessels,the testing system for gas explosion in linked vessels is established.The experiment results reveal the enhancement mechanism of gas explosion in linked vessels.The conclusions provided important reference in engineering for safe design of gas explosion venting in linked vessels.
Small Cell Association with Networked Flying Platforms: Novel Algorithms and Performance Bounds

Fifth generation (5G) and beyond-5G (B5G) systems expect coverage and capacity enhancements along with the consideration of limited power, cost and spectrum. Densification of small cells (SCs) is a promising approach to cater these demands of 5G and B5G systems. However, such an ultra dense network of SCs requires provision of smart backhaul and fronthaul networks. In this paper, we employ a scalable idea of using networked flying platforms (NFPs) as aerial hubs to provide fronthaul connectivity to the SCs. We consider the association problem of SCs and NFPs in a SC network and study the effect of practical constraints related to the system and NFPs. Mainly, we show that the association problem is related to the generalized assignment problem (GAP). Using this relation with the GAP, we show the NP-hard complexity of the association problem and further derive an upper bound for the maximum achievable sum data rate. Linear Programming relaxation of the problem is also studied to compare the results with the derived bounds. Finally, two efficient (less complex) greedy solutions of the association problem are presented, where one of them is a distributed solution and the other one is its centralized version. Numerical results show a favorable performance of the presented algorithms with respect to the exhaustive search and derived bounds. The computational complexity comparison of the algorithms with the exhaustive search is also presented to show that the presented algorithms can be practically implemented.
Reproductive performance in male chickens fed protein deficient diets during the growing period.

Abstract LOW LEVELS of dietary protein have been found to delay sexual maturity in pullets (Waldroup and Harms, 1962). Arscott and Parker (1963) stated that adult males fed 6.9% protein had higher fertility than the males fed 10.7% or 16.0% protein; there was no effect on hatchability. Wilson et al. (1965) found that body growth was inversely related to the level of dietary protein when levels of 16.0, 9.0, 6.75 and 4.5% were fed during the growing period. Sexual maturity was delayed in the low protein groups, but after being fed a 17.0% protein diet for 7 weeks sperm concentrations were about equal in all groups. Fertility was higher in the males which had been fed 9.0 and 6.75% protein during the growing period. Hatchability of fertile eggs was not affected by the level of protein fed. The following experiments were designed to study the effects of low dietary protein during .
Characterization of an alcoholic hepatic steatosis model induced by ethanol and high-fat diet in rats

Alcoholic liver disease is characterized by a wide spectrum of liver damage, which increases when ethanol is associated with high-fat diets (HFD). This work aimed to establish a model of alcoholic hepatic steatosis (AHS) by using a combination of 10% ethanol and sunflower seeds as the source of HFD. Male rats received water or 10% ethanol and regular chow diet and/or HFD, which consisted of sunflower seeds. The food consumption, liquid intake and body weight of the rats were monitored for 30 days. After this period, blood was collected for biochemical evaluation, and liver samples were collected for histological, mitochondrial enzyme activity and oxidative stress analyses. Our results indicated that the combination of 10% ethanol and HFD induced micro- and macrosteatosis and hepatocyte tumefaction, decreased the levels of reduced glutathione and glutathione S-transferase activity and increased the level of lipoperoxidation and superoxide dismutase activity. The mitochondrial oxidation of NADH and succinate were partially inhibited. Complexes I and II were the main inhibition sites. Hepatic steatosis was successfully induced after 4 weeks of the diet, and the liver function was modified. The combination of 10% ethanol and sunflower seeds as an HFD produced an inexpensive model to study AHS in rats.