Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal (and benchmark-optimal) competition complexity for additive buyers over independent items

The Competition Complexity of an auction setting refers to the number of additional bidders necessary in order for the (deterministic, prior-independent, dominant strategy truthful) Vickrey-Clarke-Groves mechanism to achieve greater revenue than the (randomized, prior-dependent, Bayesian-truthful) optimal mechanism without the additional bidders. We prove that the competition complexity of n bidders with additive valuations over m independent items is at most n(ln(1+m/n)+2), and also at most 9√nm. When n ≤ m, the first bound is optimal up to constant factors, even when the items are i.i. d. and regular. When n ≥ m, the second bound is optimal for the benchmark introduced by Eden et al. up to constant factors, even when the items are i.i. d. and regular. We further show that, while the Eden et al. benchmark is not necessarily tight in the n ≥ m regime, the competition complexity of n bidders with additive valuations over even 2 i.i. d. regular items is indeed ω(1). Our main technical contribution is a reduction from analyzing the Eden et al. benchmark to proving stochastic dominance of certain random variables.
Disruption in time projection and non-adherence to long-term therapies

Objective Patients’ non-adherence to medical prescriptions is a crucial issue in contemporary medicine because it can jeopardize care efficacy. Non-adherence is especially frequent in patients with chronic diseases. In this article, we propose that a particular condition, which we call disruption in time projection, is a cause of non-adherence to medication therapies in chronic diseases. Methods A questionnaire was administered to 120 hospitalized people with type 2 diabetes addressing three psychological constructs defining time projection: patience/impatience in a fictive monetary scenario (preferring to receive €1,500 in 1 year or €500 today), magnitude of temporal horizon (greater or lesser ability to imagine future events) and perception of the degree of physical similarity of current self to self at 1 year, 5 years and 10 years from the present. In addition, the questionnaire evaluated adherence to medication, social deprivation and depression. Results In the multivariate analyses, two factors were associated with adherence to medication: patience (P<0.001) and long temporal horizon (P=0.006). Two factors were associated with HbA1c ≥8% (64 mmol/mol): non-adherence to medication (P=0.003) and short temporal horizon (P=0.011). Three factors were associated with long temporal horizon: adherence to medication (P<0.001), patience (P<0.001) and the existence of grandchildren (P=0.002). Social deprivation (P<0.001), non-adherence (P<0.001), female gender (P=0.002) and short temporal horizon (P=0.050) were associated with impatience. Finally, an association of adherence to expected similarity in the future to current self, impatience, short temporal horizon, social deprivation and depression was also shown in a multiple correspondence analysis. Conclusion What we termed a disruption in time projection may be a unique determinant for non-adherence to long-term therapy and, therefore, may influence the outcome of chronic diseases. We hypothesize that this is involved in both intentional and unintentional non-adherence and that it represents the loss of a protective mechanism. If this novel concept is to be confirmed in other settings and generalized to other chronic diseases, the recognition of its role in disease prognosis may help orient the teaching and practice of medicine.
Evaluation of RETICs Glaucoma Diagnostic Calculators in Preperimetric Glaucoma

Purpose To evaluate two glaucoma diagnostic calculators (GDC) in a group of eyes with preperimetric glaucoma (PPG). Methods All eyes (n = 265) included in this study had ocular hypertension with normal visual fields (VFs) on repeated VF tests. PPG was defined as progression in the Guided Progression Analysis software from Cirrus-optical coherence tomography (GPA-OCT). Three PPG types were defined according to the GPA-OCT software as follows: (1) GPA-OCT with one or more red boxes in two or more columns; (2) GPA-OCT with two or more red boxes in two or more columns; and (3) GPA-OCT with two or more red boxes in two or more columns (definition 2), and in the last scan one or more red box in the RNFL average or quadrants. Nonparametric tests, areas under the receiver operating characteristic curve (AUC), and Bland-Altman tests were assessed. Results Definitions one, two, and three were met by 44 (16.6%), 29 (10.9%), and 11 (4.2%) eyes, respectively. The GDC indices (means ± standard deviations) were, respectively, 14.49 ± 21.55% and 26.06 ± 22.50% using the combined and quantitative GDC (P < 0.001) in all eyes. Both GDC showed higher glaucoma probability in the PPG group (P < 0.04; combined GDC AUCs, 0.720–0.833; quantitative GDC AUCs, 0.700–0.839). GDC values were higher (P < 0.01) with greater GPA progression. Conclusions The values of both GDC were higher in the PPG group than the ocular hypertension group. The GDC were higher when more columns in the GPA software indicated progression. Both GDC showed a similar ability to detect PPG. Translational Relevance These calculators facilitate diagnosis of PPG in ocular hypertensive eyes.
Evaluation of modeling strategies for assessing self‐thinning behavior and carrying capacity

Abstract Self‐thinning and site maximum carrying capacity are key concepts for understanding and predicting ecosystem dynamics as they represent the outcome of several fundamental ecological processes (e.g., mortality and growth). Relationships are often derived using alternative modeling strategies, depending on the statistical approach, model formulation, and underlying data with unclear implications of these various assumptions. In this analysis, the influence of contrasting modeling strategies for estimating the self‐thinning relationship and maximum carrying capacity in long‐term, permanent plot data (n = 130) from the mixed Nothofagus forests in southern Chile was assessed and compared. Seven contrasting modeling strategies were used including ordinary least squares, quantile, and nonlinear regression that were formulated based on static (no remeasurements) or dynamic data (with remeasurements). Statistically distinct differences among these seven approaches were identified with mean maximum carrying capacity ranging from 1,050 to 1,912 stems/ha depending on the approach. The population‐level static approach based on quantile regression produced an estimate closest to the overall mean with site‐level carrying capacity depending on tree species diversity and climate. Synthesis and applications. Overall, the findings highlight strong variability within and between contrasting methods of determining self‐thinning and site maximum carry capacity, which may influence ecological inferences.
Drug-resistance profiling and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis in Saudi Arabia revealed by whole genome sequencing

Background In Saudi Arabia, cross-border transmission of multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains might be particularly fostered by high immigration rates. Herein, we aimed to elucidate the transmission dynamics of MDR-MTBC strains and reveal a detailed prediction of all resistance-conferring mutations for the first- and second-line drugs. Methods We investigated all MDR-MTBC strains collected between 2015 and 2017 from provincial mycobacteria referral laboratories and compared demographic and clinical parameters to a cohort of non-MDR-TB patients using a whole genome sequencing approach. Clusters were defined based on a maximum strain-to-strain genetic distance of five single-nucleotide polymorphisms (SNPs) as surrogate marker for recent transmission, and then investigated molecular drug-resistance markers (37 genes). Results Forty-eight (67.6%) MDR-MTBC strains were grouped in 14 different clusters, ranging in size from two to six strains; 22.5% (16/71) of all MDR-MTBC isolates were predicted to be fully resistant to all five first-line drugs, and five strains (7.0%) exhibited fluoroquinolone resistance. Moreover, we revealed the presence of 12 compensatory mutations as well as 26 non-synonymous SNPs in the rpoC gene and non-hotspot region in rpoB, respectively Conclusion Optimized TB molecular surveillance, diagnosis, and patient management are urgently needed to contain MDR-MTBC transmission and prevent the development of additional drug resistance.
Comprehensive Analysis of BAP1 Somatic Mutation in Clear Cell Renal Cell Carcinoma to Explore Potential Mechanisms in Silico

Purpose: Aim of this study was to comprehensively analyze BRCA1-associated protein-1 (BAP1) somatic mutation in clear cell renal cell carcinoma (ccRCC) and explore potential therapeutic pathways and molecules. Patients and methods: In this study, we analyzed 445 ccRCC cases from The Cancer Genome Atlas (TCGA). Comprehensive analysis including survival, transcriptome and methylation between BAP1 mutated and wild-type cases was performed using bioinformatics tools in silico. Pathways and molecules related to BAP1 mutation were analyzed using Database for Annotation, Visualization and Integrated Discovery (DAVID) and protein-protein interaction (PPI) network. Results: BAP1 mutated ccRCC patients had a worse overall survival (OS) and disease free survival (DFS) than BAP1 wild-type patients. We found 583 up-regulated and 1216 down-regulated different expressed genes (DEGs) in BAP1 mutated tumors. Up-regulated DEGs were enriched in molecular functions and biological processes like protein binding, protein transport and ubiquitin protein ligase binding. Down-regulated DEGs were enriched in pathways like Rap1 signaling pathway, Notch pathway and altered molecular functions like metal ion binding and ubiquitin-protein transferase activity. Furthermore, CAD, TSPO, CTNNB1 and MAPK3 were top hub genes selected using PPI network analysis. Finally, BAP1 mutation had a strong correlation with CpG island methylator phenotype (CIMP). Conclusion: Our study provides a comprehensive understanding of BAP1 functional somatic mutation in ccRCC patients. Several hub genes like CAD and TSPO may become potential therapeutic targets.
A Comparison of Automatic Differentiation and Continuous Sensitivity Analysis for Derivatives of Differential Equation Solutions

Derivatives of differential equation solutions are commonly for parameter estimation, fitting neural differential equations, and as model diagnostics. However, with a litany of choices and a Cartesian product of potential methods, it can be difficult for practitioners to understand which method is likely to be the most effective on their particular application. In this manuscript we investigate the performance characteristics of Discrete Local Sensitivity Analysis implemented via Automatic Differentiation (DSAAD) against continuous adjoint sensitivity analysis. Non-stiff and stiff biological and pharmacometric models, including a PDE discretization, are used to quantify the performance of sensitivity analysis methods. Our benchmarks show that on small stiff and non-stiff systems of ODEs (approximately < 100 parameters+ODEs), forward-mode DSAAD is more efficient than both reverse-mode and continuous forward/adjoint sensitivity analysis. The scalability of continuous adjoint methods is shown to be more efficient than discrete adjoints and forward methods after crossing this size range. These comparative studies demonstrate a trade-off between memory usage and performance in the continuous adjoint methods that should be considered when choosing the technique, while numerically unstable backsolve techniques from the machine learning literature are demonstrated as unsuitable for most scientific models. The performance of adjoint methods is shown to be heavily tied to the reverse-mode AD method used for the vector-Jacobian product calculations, with tape-based AD methods shown to be 2 orders of magnitude slower on nonlinear partial differential equations than static AD techniques. In addition, these results demonstrate the out-of-the-box applicability of DSAAD to differential-algebraic equations, delay differential equations, and hybrid differential equation systems where the event timing and effects are dependent on model parameters, showcasing an ease of implementation advantage for DSAAD approaches. Together, these benchmarks provide a guide to help practitioners to quickly identify the best mixture of continuous sensitivities and automatic differentiation for their applications.
Curcumin nanoemulsion as a novel chemical for the treatment of acute and chronic toxoplasmosis in mice

Background The aim of this study was to prepare curcumin nanoemulsion (CR-NE) to solve the problems associated with poor water solubility and low bioavailability of CR and to test its efficiency in the treatment of acute and chronic toxoplasmosis in mouse models. Materials and methods CR-NE 1% was prepared using spontaneous emulsification by soybean as oil phase; a mixture of Tween 80 and Tween 85 as surfactant; ethanol as cosurfactant and distilled water. Particle size and zeta potential of NE were assessed using Nano-ZS90 dynamic light scattering. Stability testing of NE was assessed after storage for 2 months at room temperature. In vivo experiments were carried out using 50 BALB/c mice inoculated with virulent RH strain (type I) and 50 BALB/c mice inoculated with avirulent Tehran strain (type II) of Toxoplasma gondii and treated with CR-NE (1% w/v), CR suspension (CR-S, 1% w/v), and NE without CR (NE-no CR). Results The mean particle size and zeta potential of CR-NE included 215.66±16.8 nm and −29.46±2.65 mV, respectively, and were stable in particle size after a three freeze–thaw cycle. In acute phase experiment, the survival time of mice infected with RH strain of T. gondii and treated with CR-NE extended from 8 to 10 days postinoculation. The differences were statistically significant between the survival time of mice in CR-NE-treated group compared with negative control group (P<0.001). Furthermore, CR-NE significantly decreased the mean counts of peritoneum tachyzoites from 5,962.5±666 in negative control group to 627.5±73 in CR-NE-treated mice (P<0.001). Growth inhibition rates of tachyzoites in peritoneum of mice receiving CR-NE, CR-S, and NE-no CR included 90%, 21%, and 11%, respectively, compared with negative control group. In chronic phase experiment, the average number and size of tissue cysts significantly decreased to 17.2±15.6 and 31.5±6.26 µm, respectively, in mice inoculated with bradyzoites of T. gondii Tehran strain and treated with CR-NE compared with that in negative control group (P<0.001). Decrease of cyst numbers was verified by downregulation of BAG1 in treatment groups compared with negative control group with a minimum relative expression in CR-NE (1.12±0.28), CR-S (11.76±0.87), and NE-no CR (14.67±0.77), respectively, (P<0.001). Conclusion Results from the current study showed the potential of CR-S and CR-NE in treatment of acute and chronic toxoplasmosis in mouse models for the first time. However, CR-NE was more efficient than CR-S, and it seems that CR-NE has a potential formula for the treatment of acute and chronic toxoplasmosis, especially in those with latent bradyzoites in brain.
Hospitalized Pets as a Source of Carbapenem-Resistance

The massive and irrational use of antibiotics in livestock productions has fostered the occurrence and spread of resistance to “old class antimicrobials. ” To cope with that phenomenon, some regulations have been already enforced in the member states of the European Union. However, a role of livestock animals in the relatively recent alerts on the rapid worldwide increase of resistance to last-choice antimicrobials as carbapenems is very unlikely. Conversely, these antimicrobials are increasingly administered in veterinary hospitals whose role in spreading bacteria or mobile genetic elements has not adequately been addressed so far. A cross-sectional study was carried out on 105 hospitalized and 100 non-hospitalized pets with the aim of measuring the prevalence of carbapenem-resistant Gram-negative bacteria (GNB) colonizing dogs and cats, either hospitalized or not hospitalized and estimating the relative odds. Stool samples were inoculated on MacConkey agar plates containing 1 mg/L imipenem which were then incubated aerobically at 37°C ± 1 for 48 h. Isolated bacteria were identified first by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and were confirmed by 16S rRNA sequencing. The genetic basis of resistance was investigated using PCR methods, gene or whole genome sequencing (WGS). The prevalence of pets harboring carbapenem-resistant bacteria was 11.4 and 1.0% in hospitalized and not-hospitalized animals, respectively, with an odds ratio of 12.8 (p < 0.01). One pet carried two diverse isolates. Overall, 14 gram-negative non-fermenting bacteria, specifically, one Acinetobacter radioresistens, five Acinetobacter baumannii, six Pseudomonas aeruginosa and two Stenotrophomonas maltophilia were isolated. The Acinetobacter species carried acquired carbapenemases genes encoded by blaNDM-1 and blaOXA-23. In contrast, Pseudomonas phenotypic resistance was associated with the presence of mutations in the oprD gene. Notably, inherent carbapenem-resistant isolates of S. maltophilia were also resistant to the first-line recommended chemotherapeutic trimethoprim/sulfamethoxazole. This study estimates the risk of colonization by carbapenem-resistant non-fermenting GNB in pets hospitalized in veterinary tertiary care centers and highlights their potential role in spreading resistance genes among the animal and human community. Public health authorities should consider extending surveillance systems and putting the release of critical antibiotics under more strict control in order to manage the infection/colonization of pets in veterinary settings.
DropPruning for Model Compression

Deep neural networks (DNNs) have dramatically achieved great success on a variety of challenging tasks. However, most of the successful DNNs are structurally so complex, leading to much storage requirement and floating-point operation. This paper proposes a novel technique, named Drop Pruning, to compress the DNNs by pruning the weights from a dense high-accuracy baseline model without accuracy loss. Drop Pruning also falls into the standard iterative prune-retrain procedure, where a \emph{drop} strategy exists at each pruning step: \emph{drop out}, stochastic deleting some unimportant weights and \emph{drop in}, stochastic recovering some pruned weights. \emph{Drop out} and \emph{drop in} are supposed to handle the two drawbacks of the traditional pruning methods: local importance judgment and irretrievable pruning process, respectively. The suitable choosing of \emph{drop} probabilities can decrease the model size during pruning process and lead it to flow to the target sparsity. Drop Pruning also has some similar spirits with dropout, a stochastic algorithm in Integer Optimization and the Dense-Sparse-Dense training technique. Drop Pruning can significantly reducing overfitting while compressing the model. Experimental results demonstrates that Drop Pruning can achieve the state-of-the-art performance on many benchmark pruning tasks, about ${11.1\times}$ compression of VGG-16 on CIFAR10 and ${14.3\times}$ compression of LeNet-5 on MNIST without accuracy loss, which may provide some new insights into the aspect of model compression.
Maternal age effects on fecundity and offspring egg‐to‐adult viability are not affected by mitochondrial haplotype

Abstract While numerous studies have demonstrated that mitochondrial genetic variation can shape organismal phenotype, the level of contribution the mitochondrial genotype makes to life‐history phenotype across the life course remains unknown. Furthermore, a clear technical bias has emerged in studies of mitochondrial effects on reproduction, with many studies conducted on males, but few on females. Here, we apply a classic prediction of the evolutionary theory of aging to the mitochondrial genome, predicting the declining force of natural selection with age will have facilitated the accumulation of mtDNA mutations that confer late‐life effects on female reproductive performance. This should lead to increased levels of mitochondrial genetic variation on reproduction at later‐life stages. We tested this hypothesis using thirteen strains of Drosophila melanogaster that each possessed a different mitochondrial haplotype in an otherwise standard nuclear genetic background. We measured fecundity and egg‐to‐adult viability of females over five different age classes ranging from early to late life and quantified the survival of females throughout this time period. We found no significant variation across mitochondrial haplotypes for the reproductive traits, and no mitochondrial effect on the slope of decline in these traits with increasing age. However, we observed that flies that died earlier in the experiment experienced steeper declines in the reproductive traits prior to death, and we also identified maternal and grandparental age effects on the measured traits. These results suggest the mitochondrial variation does not make a key contribution to shaping the reproductive performance of females.
Postpartum family-planning barriers and catalysts in Burkina Faso and the Democratic Republic of Congo: a multiperspective study

Purpose To address the high unmet need for postpartum family planning (PPFP) in resource-limited settings, particularly in sub-Saharan Africa, this study aimed to identify PPFP-related barriers and catalysts to inform policies and programs to increase access to postpartum contraception. Methods Using qualitative methodology, we explored the perspectives of women, adolescent girls, men, religious and community leaders, service providers, and decision makers from three rural communities in Burkina Faso and three rural–urban communities in the Democratic Republic of Congo. Both countries have high unmet need for PPFP and are priority countries of the French Muskoka Fund for Maternal and Child Health. Results Perceived catalysts included negative traditional views on the consequences borne by closely spaced children and their mothers; a 6-week postpartum visit dedicated to PPFP (albeit poorly attended); political will and enabling policies for FP; and support from certain religious leaders and men. Main reported barriers were the lack of male engagement; out-of-pocket copayment for contraceptives; reliance on amenorrhea for pregnancy prevention without knowing its limits; misconceptions about modern contraceptives, including prerequisites for the lactational amenorrhea method; sexual abstinence supported by religious and traditional norms for up to 3–6 months, although women reported earlier resumption of sexual activity; low prioritization of scheduled postpartum visits by women; and limited availability of readily accessible methods, PPFP counseling materials, and clinic days and scheduled visits dedicated to contraceptive services. Conclusion Based on results found to be most actionable, the following interventions have the potential to optimize access to PPFP services: counseling women on postpartum-pregnancy risks and options at different points in time before and after childbirth through the use of appropriate information, education, and counseling materials; integrating PPFP services into existing maternal and child health visits; making contraceptives readily available and affordable; and meaningfully engaging male partners.