Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-rank singular value thresholding for recovering missing air quality data

With the increasing awareness of the harmful impacts of urban air pollution, air quality monitoring stations have been deployed in many metropolitan areas. These stations provide air quality data to the public. However, due to sampling device failures and data processing errors, missing data in air quality measurements is common. Data integrity becomes a critical challenge when such data are employed for public services. In this paper, we investigate the mathematical property of air quality measurements, and attempt to recover the missing data. First, we empirically study the low rank property of these measurements. Second, we formulate the low rank matrix completion (LRMC) optimization problem to reconstruct the missing air quality data. The problem is transformed using duality theory, and singular value thresholding (SVT) is employed to develop sub-optimal solutions. Third, to evaluate the performance of our methodology, we conduct a series of case studies including different types of missing data patterns. The simulation results demonstrate that the proposed SVT methodology can effectively recover missing air quality data, and outperform the existing Interpolation. Finally, we investigate the parameter sensitivity of SVT. Our study can serve as a guideline for missing data recovery in the real world.
Asymmetric Positron Interactions with Chiral Quartz Crystals?

We have studied the interaction of the positron with chiral left-or right-handed quartz crystals. In Doppler-broadening experiments, using a mono-energetic positron beam there is a differential depth profile for positrons implanted in LH or RH z-cut quartz as identified by a shape parameter (S). Further, in bulk positron annihilation lifetime spectroscopy (PALS) experiments, the lifetime (τ 2) attributed to free annihilation of the positron interacting with the chiral lattice exhibits a larger value for the LH quartz, and the associated intensity (I2) is also significantly different—RH quartz is consistently 10% greater than the LH crystal. The τ3 lifetime and its intensity, I3, attributed to positronium interacting with defects in the quartz, also appears to exhibit differences between the enantiomeric sets of crystals. These observations may demonstrate chiral recognition using a positron annihilation technique, pave the way for a broad range of positron experiments, and may help inform hypotheses of chirality recognition, selection, or induction by beta radiation.
Surface sensitivity of four-probe STM for the measurement of the resistivity of bulk ZnO correlated to XPS.

Multi-probe instruments based on scanning tunnelling microscopy (STM) are becoming increasingly common for their ability to perform nanoto atomic-scale investigations of nanostructures, surfaces and in situ reactions. A common configuration is the four-probe STM often coupled with in situ scanning electron microscopy (SEM) that allows precise positioning of the probes onto surfaces and nanostructures enabling electrical and scanning experiments to be performed on highly localised regions of the sample. In this paper, we assess the sensitivity of four-probe STM for in-line resistivity measurements of the bulk ZnO surface. The measurements allow comparisons to established models that are used to relate light plasma treatments (O and H) of the surfaces to the resistivity measurements. The Page 1 of 25 AUTHOR SUBMITTED MANUSCRIPT JPCM-109333.R1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 results are correlated to x-ray photoelectron spectroscopy (XPS) and show that four-probe STM can detect changes in surface and bulk conduction mechanisms that are beyond conventional monochromatic XPS.
Evolocumab and Clinical Outcomes in Patients with Cardiovascular Disease

BACKGROUND Evolocumab is a monoclonal antibody that inhibits proprotein convertase subtilisin–kexin type 9 (PCSK9) and lowers low‐density lipoprotein (LDL) cholesterol levels by approximately 60%. Whether it prevents cardiovascular events is uncertain. METHODS We conducted a randomized, double‐blind, placebo‐controlled trial involving 27,564 patients with atherosclerotic cardiovascular disease and LDL cholesterol levels of 70 mg per deciliter (1.8 mmol per liter) or higher who were receiving statin therapy. Patients were randomly assigned to receive evolocumab (either 140 mg every 2 weeks or 420 mg monthly) or matching placebo as subcutaneous injections. The primary efficacy end point was the composite of cardiovascular death, myocardial infarction, stroke, hospitalization for unstable angina, or coronary revascularization. The key secondary efficacy end point was the composite of cardiovascular death, myocardial infarction, or stroke. The median duration of follow‐up was 2.2 years. RESULTS At 48 weeks, the least‐squares mean percentage reduction in LDL cholesterol levels with evolocumab, as compared with placebo, was 59%, from a median baseline value of 92 mg per deciliter (2.4 mmol per liter) to 30 mg per deciliter (0.78 mmol per liter) (P<0.001). Relative to placebo, evolocumab treatment significantly reduced the risk of the primary end point (1344 patients [9.8%] vs. 1563 patients [11.3%]; hazard ratio, 0.85; 95% confidence interval [CI], 0.79 to 0.92; P<0.001) and the key secondary end point (816 [5.9%] vs. 1013 [7.4%]; hazard ratio, 0.80; 95% CI, 0.73 to 0.88; P<0.001). The results were consistent across key subgroups, including the subgroup of patients in the lowest quartile for baseline LDL cholesterol levels (median, 74 mg per deciliter [1.9 mmol per liter]). There was no significant difference between the study groups with regard to adverse events (including new‐onset diabetes and neurocognitive events), with the exception of injection‐site reactions, which were more common with evolocumab (2.1% vs. 1.6%). CONCLUSIONS In our trial, inhibition of PCSK9 with evolocumab on a background of statin therapy lowered LDL cholesterol levels to a median of 30 mg per deciliter (0.78 mmol per liter) and reduced the risk of cardiovascular events. These findings show that patients with atherosclerotic cardiovascular disease benefit from lowering of LDL cholesterol levels below current targets. (Funded by Amgen; FOURIER ClinicalTrials.gov number, NCT01764633.)
Current therapies and mortality in acromegaly

Acromegaly is a rare disease most frequently due to a GH secreting pituitary adenoma. Without an appropriate therapy, life of patients with acromegaly can be shortened with ten years. Pituitary surgery is usually the first line therapy for GH secreting pituitary adenomas. A meta-analysis proved that mortality is much lower in operated patients, even uncured, than the entire group of patients and is similar with the general population in patients with GH<1 μg/ L. For the patients with hypersecreting postoperative remnant tumor, those with low chance of surgical cure or with life-threatening comorbidities, medical therapies are available: somatostatin receptor analogues (SRA), dopamine agonists (DA) and GH receptor antagonists. Studies with >30% utilization of SRAs reported a lower mortality ratio than studies with lower percentages of SRA administration. Although therapy with DA has long been used in patients with acromegaly, there are no studies reporting its effect on mortality, but its efficacy is limited by the low remission rate obtained. The use of conventional external radiotherapy, although with good remission rate in time, was linked with increased mortality, mostly due to cerebrovascular diseases. Conclusion. Mortality in acromegaly can be reduced to expected levels from general population by using modern therapies either in monotherapy or by using multimodal approaches in experienced centers.
The Genetic Variation of RELN Expression in Schizophrenia and Bipolar Disorder

Reelin plays an important role in the development and function of the brain and has been linked to different neuropsychiatric diseases. To further clarify the connection between reelin and psychiatric disorders, we studied the factors that influence the expression of reelin gene (RELN) and its different isoforms. We examined the total expression of RELN, allelic expression, and two alternative RELN isoforms in postmortem brain samples from patients with schizophrenia and bipolar disorder, as well as unaffected controls. We did not find a significant reduction in the total expression of RELN in schizophrenia or bipolar disorder. However, we did find a significant reduction of the proportion of the short RELN isoform, missing the C-terminal region in bipolar disorder, and imbalance in the allelic expression of RELN in schizophrenia. In addition, we tested the association between variation in RELN expression and rs7341475, an intronic SNP that was found to be associated with schizophrenia in women. We did not find an association between rs7341474 and the total expression of RELN either in women or in the entire sample. However, we observed a nominally significant effect of genotype-by-sex interaction on the variation in microexon skipping. Women with the risk genotype of rs7341475 (GG) had a higher proportion of microexon skipping, which is the isoform predominant in tissues outside the brain, while men had the opposite trend. Finally, we tested 83 SNPs in the gene region for association with expression variation of RELN, but none were significant. Our study further supports the connection between RELN dysfunction and psychiatric disorders, and provides a possible functional role for a schizophrenia associated SNP. Nevertheless, the positive associations observed in this study needs further replication as it may have implications for understanding the biological causes of schizophrenia and bipolar disorder.
Measurement of central corneal thickness by high‐resolution Scheimpflug imaging, Fourier‐domain optical coherence tomography and ultrasound pachymetry

Purpose: To compare the repeatability and reproducibility of central corneal thickness (CCT) measurements by high‐resolution (HR) rotating Scheimpflug imaging and Fourier‐domain optical coherence tomography (FD‐OCT). CCT measurements were compared to those determined by ultrasound pachymetry (UP).
High Content Phenotypic Cell-Based Visual Screen Identifies Mycobacterium tuberculosis Acyltrehalose-Containing Glycolipids Involved in Phagosome Remodeling

The ability of the tubercle bacillus to arrest phagosome maturation is considered one major mechanism that allows its survival within host macrophages. To identify mycobacterial genes involved in this process, we developed a high throughput phenotypic cell-based assay enabling individual sub-cellular analysis of over 11,000 Mycobacterium tuberculosis mutants. This very stringent assay makes use of fluorescent staining for intracellular acidic compartments, and automated confocal microscopy to quantitatively determine the intracellular localization of M. tuberculosis. We characterised the ten mutants that traffic most frequently into acidified compartments early after phagocytosis, suggesting that they had lost their ability to arrest phagosomal maturation. Molecular analysis of these mutants revealed mainly disruptions in genes involved in cell envelope biogenesis (fadD28), the ESX-1 secretion system (espL/Rv3880), molybdopterin biosynthesis (moaC1 and moaD1), as well as in genes from a novel locus, Rv1503c-Rv1506c. Most interestingly, the mutants in Rv1503c and Rv1506c were perturbed in the biosynthesis of acyltrehalose-containing glycolipids. Our results suggest that such glycolipids indeed play a critical role in the early intracellular fate of the tubercle bacillus. The unbiased approach developed here can be easily adapted for functional genomics study of intracellular pathogens, together with focused discovery of new anti-microbials.
Characterization of the interaction partners of secreted proteins and chaperones of Shigella flexneri

The type III secretion (TTS) system of Gram‐negative pathogenic bacteria is composed of proteins that assemble into the TTS machinery, proteins that are secreted by this machinery and specific chaperones that are required for storage and sometimes secretion of these proteins. Many sequential protein interactions are involved in the TTS pathway to deliver effector proteins to host cells. We used the yeast two‐hybrid system to investigate the interaction partners of the Shigella flexneri effectors and chaperones. Libraries of preys containing random fusions with fragments of the TTS proteins were screened using effectors and chaperones as baits. Interactions between the effectors IpaB and IpaC and their chaperone IpgC were detected by this method, and interaction domains were identified. Using a His‐tagged IpgC protein to co‐purify truncated IpaB and IpaC proteins, we showed that the chaperone‐binding domain was unique and located in the N‐terminus of these proteins. This domain was not required for the secretion of recombinant proteins but was involved in the stability of IpaC and instability of IpaB. Homotypic interactions were identified with the baits IpaA, IpaB and IpaC. Interactions between effectors and components of the TTS machinery were also selected that might give insights into regulation of the TTS process.
Experience-Induced Neurogenesis in the Senescent Dentate Gyrus

We demonstrate here that under physiological conditions neurogenesis continues to occur in the dentate gyrus of senescent mice and can be stimulated by living in an enriched environment. Neurogenesis was investigated by confocal microscopy of three-channel immunofluorescent staining for the proliferation marker bromodeoxyuridine (BrdU) and neuronal and glial markers. Quantification was performed with unbiased stereological counting techniques. Neurogenesis decreased with increasing age. Stimulation of adult and aged mice by switching from standard housing to an enriched environment with opportunities for social interaction, exploration, and physical activity for 68 d resulted in an increased survival of labeled cells. Phenotypic analysis revealed that, in enriched living animals, relatively more cells differentiated into neurons, resulting in a threefold net increase of BrdU-labeled neurons in 20-month-old mice (105 vs 32 cells) and a more than twofold increase in 8-month-old mice (684 vs 285 cells) compared with littermates living under standard laboratory conditions. Corresponding absolute numbers of BrdU-positive astrocytes and BrdU-positive cells that did not show colabeling for neuronal or glial markers were not influenced. The effect on the relative distribution of phenotypes can be interpreted as a survival-promoting effect that is selective for neurons. Proliferation of progenitor cells appeared unaffected by environmental stimulation.
Nervous system–derived chondroitin sulfate proteoglycans regulate growth cone morphology and inhibit neurite outgrowth: A light, epifluorescence, and electron microscopy study

Proteoglycans influence aging and plasticity in the nervous system. Particularly prominent are the chondroitin sulfate proteoglycans (CSPGs), which are generally inhibitory to neurite outgrowth. During development, CSPGs facilitate normal guidance, but following nervous system injury and in diseases of aging (e.g., Alzheimer's disease), they block successful regeneration, and are associated with axon devoid regions and degenerating nerve cells. Whereas previous studies used non‐nervous system sources of CSPGs, this study analyzed the morphology and behavior of sensory (dorsal root ganglia) neurons, and a human nerve cell model (SH‐SY5Y neuroblastoma cells) as they contacted nervous system–derived CSPGs, using a variety of microscopy techniques. The results of these qualitative analyses show that growth cones of both nerve cell types contact CSPGs via actin‐based filopodia, sample the CSPGs repeatedly without collapse, and alter their trajectory to avoid nervous system–derived CSPGs. Turning and branching are correlated with increased filopodial sampling, and are common to both neurons and Schwann cells. We show that CSPG expression by rat CNS astrocytes in culture is correlated with sensory neuron avoidance. Further, we show for the first time the ultrastructure of sensory growth cones at a CSPG‐laminin border and reveal details of growth cone and neurite organization at this choice point. This type of detailed analysis of the response of growth cones to nervous system–derived CSPGs may lead to an understanding of CSPG function following injury and in diseases of aging, where CSPGs are likely to contribute to aberrant neurite outgrowth, failed or reduced synaptic connectivity, and/or ineffective plasticity. Microsc. Res. Tech. 54:273–286, 2001. © 2001 Wiley‐Liss, Inc.
T Cells Enhance Stem-Like Properties and Conditional Malignancy in Gliomas

Background Small populations of highly tumorigenic stem-like cells (cancer stem cells; CSCs) can exist within, and uniquely regenerate cancers including malignant brain tumors (gliomas). Many aspects of glioma CSCs (GSCs), however, have been characterized in non-physiological settings. Methods We found gene expression similarity superiorly defined glioma “stemness”, and revealed that GSC similarity increased with lower tumor grade. Using this method, we examined stemness in human grade IV gliomas (GBM) before and after dendritic cell (DC) vaccine therapy. This was followed by gene expression, phenotypic and functional analysis of murine GL26 tumors recovered from nude, wild-type, or DC-vaccinated host brains. Results GSC similarity was specifically increased in post-vaccine GBMs, and correlated best to vaccine-altered gene expression and endogenous anti-tumor T cell activity. GL26 analysis confirmed immune alterations, specific acquisition of stem cell markers, specifically enhanced sensitivity to anti-stem drug (cyclopamine), and enhanced tumorigenicity in wild-type hosts, in tumors in proportion to anti-tumor T cell activity. Nevertheless, vaccine-exposed GL26 cells were no more tumorigenic than parental GL26 in T cell-deficient hosts, though they otherwise appeared similar to GSCs enriched by chemotherapy. Finally, vaccine-exposed GBM and GL26 exhibited relatively homogeneous expression of genes expressed in progenitor cells and/or differentiation. Conclusions T cell activity represents an inducible physiological process capable of proportionally enriching GSCs in human and mouse gliomas. Stem-like gliomas enriched by strong T cell activity, however, may differ from other GSCs in that their stem-like properties may be disassociated from increased tumor malignancy and heterogeneity under specific host immune conditions.
Nutrigenomics of Body Weight Regulation: A Rationale for Careful Dissection of Individual Contributors

Body weight stability may imply active regulation towards a certain physiological condition, a body weight setpoint. This interpretation is ill at odds with the world-wide increase in overweight and obesity. Until now, a body weight setpoint has remained elusive and the setpoint theory did not provide practical clues for body weight reduction interventions. For this an alternative theoretical model is necessary, which is available as the settling point model. The settling point model postulates that there is little active regulation towards a predefined body weight, but that body weight settles based on the resultant of a number of contributors, represented by the individual’s genetic predisposition, in interaction with environmental and socioeconomic factors, such as diet and lifestyle. This review refines the settling point model and argues that by taking body weight regulation from a settling point perspective, the road will be opened to careful dissection of the various contributors to establishment of body weight and its regulation. This is both necessary and useful. Nutrigenomic technologies may help to delineate contributors to body weight settling. Understanding how and to which extent the different contributors influence body weight will allow the design of weight loss and weight maintenance interventions, which hopefully are more successful than those that are currently available.
Association Between Excessive Daytime Sleepiness and Functional Gastrointestinal Disorders: A Population-based Study in China

Background/Aims Several studies have demonstrated that sleep problems are associated with functional gastrointestinal disorders (FGIDs): irritable bowel syndrome (IBS), functional dyspepsia, etc, but the relationship between excessive daytime sleepiness (EDS) and FGIDs has not been systematically studied in the general population. This study aims to explore the relationship between EDS and specific types of FGIDs and the effect of the number of FGIDs on EDS. Methods A sample of 3600 individuals (aged 18–80 years) was selected from 5 regions in China using a randomized, stratified, multi-stage sampling method. EDS was measured by the Epworth Sleepiness Scale, while gastroesophageal reflux disease (GERD) and other FGIDs were assessed by Reflux Disease Questionnaire and the Rome II diagnostic criteria, respectively. Results The survey was completed by 2906 individuals (response rate: 80.72%), and 644 individuals (22.16%) had EDS. EDS was significantly associated with ulcer-like dyspepsia (OR, 2.50; 95% CI, 1.08–5.79), diarrhea-predominant IBS (OR, 2.00; 95% CI, 1.09–3.66), alternating IBS (OR, 2.32; 95% CI, 1.30–4.13), functional constipation (OR, 1.68; 95% CI, 1.20–2.35), and GERD (OR, 1.72; 95% CI, 1.08–2.72). Risk of EDS increased along with the increasing numbers of FGIDs: with 1 FGID (OR, 1.72; 95% CI, 1.37–2.15); with 2 FGIDs (OR, 2.43; 95% CI, 1.63–3.62); and with 3 or more FGIDs (OR, 3.26; 95% CI, 1.37–7.78). Conclusions FGIDs, such as ulcer-like dyspepsia, diarrhea-predominant IBS, alternating IBS, functional constipation, and GERD, were significantly associated with EDS. Those who suffered from more kinds of FGIDs were more susceptible to EDS.
Comparison of evolutionary multiobjective optimization with rference solution-based single-objective approach

In this paper, we demonstrate advantages and disadvantages of an evolutionary multiobjective optimization (EMO) approach in comparison with a reference solution-based single-objective approach through computational experiments on multiobjective 0/1 knapsack problems. The main characteristic feature of the EMO approach is that no a priori information about the decision maker's preference is assumed. The EMO approach tries to find well-distributed trade-off solutions with a wide range of objective values as many as possible. A final solution is supposed to be chosen from the obtained trade-off solutions by the decision maker. On the other hand, the reference solution-based approach utilizes the information about the decision maker's preference in the form of a reference solution. We examine whether the EMO approach can find good trade-off solutions close to an arbitrarily given reference solution. Experimental results show that good solutions are not always obtained by the EMO approach. We also examine where the reference solution-based approach can find many trade-off solutions around the given reference solution. Experimental results show that many trade-off solutions can not be obtained even when an archive population of non-dominated solutions is stored in the reference solution-based approach. Based on these observations, we suggest a hybrid approach.
MATHEMATICAL ENGINEERING TECHNICAL REPORTS Implications of contrarian and one-sided strategies for the fair-coin game

We derive some results on contrarian and one-sided strategies by Skeptic for the fair-coin game in the framework of the game-theoretic probability of Shafer and Vovk [8]. In particular, concerning the rate of convergence of the strong law of large numbers (SLLN), we prove that Skeptic can force that the convergence has to be slower than or equal to O(n−1/2). This is achieved by a very simple contrarian strategy of Skeptic. This type of result, bounding the rate of convergence from below, contrasts with more standard results of bounding the rate of SLLN from above by using momentum strategies. We also derive a corresponding one-sided result.