Miracle-dz/UniFAR-FTUs huggingface dataset:
Approaches for targeted proteomics and its potential applications in neuroscience

An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other ‘ omics ’ approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.
O N D EVI CE F EDERATED L EARNING P ERFORMANCE

Nowadays the edge devices experience the explosive growth due to improving computation power. Numerous data has been generated to record the user activities. Service provider can utilize those data to further enhance the service quality. However, as the data is extremely larger, centralized servers face great challenge to train huge data. Besides, users are sensitive to personal information in application usage data. One problem occurs that how service provider improves service quality without user application data. Hopefully, this difficulty is addressed by federated learning in conjunction with decentralized learning systems. Federated learning is a machine learning technique that involves training an algorithm across numerous decentralized edge devices that keep local data samples without transferring them. However, one critical issue of federated learning is systems heterogeneity, which has a great impact on federated learning process. When devices are heterogeneous, many issues arise: there are stragglers in the training process, meaning devices may drop out suddenly. This is hard to model. Therefore, this project is aimed to collect system measurements like memory usage, power consumption and training time, with which we can finally profile device characteristics. To measure the system parameters, Android applications are designed to implement on-device federated learning and measured to find the device characteristic. The applications can test multiple image classification datasets to get better generalization. Though promising results are obtained, there’s still a place for further improvements and research.
Environmental Regulations in the Mining Sector and Their Effect on Technological Innovation

conditional random effects Poisson model using both clustered and cluster-bootstrapped standard errors. They are robust to a NBDV model as well as a conditional “ ﬁ xed effects ” negative binomial model in some speci ﬁ cations. Results are robust to alternative moving averages, speci ﬁ cally two- and four-year moving averages of all covariates. Those regressions ﬁ nd the same, positive and signi ﬁ cant relationship between nonmarket changes in stringency and clean patent ﬁ ling using two- and four-year MAs. Detailed results are available upon request. 24 Standards have a maximum EPS value of 6/6 as compared with 4/6 and 5.2/6 for taxes and trading schemes, respectively.
GRAPHICAL GRAMMAR STUDIO AS A CONSTRAINT GRAMMAR SOLUTION FOR PART OF SPEECH TAGGING

This work presents a hybrid part of speech tagger which successfully combines a statistic model with a rule based system. The rules behave as constraints used to reduce the ambiguity of the tokens. The novelty is in the tool used for building such rules. Graphical Grammar Studio (GGS) is an open source software designed for matching/finding sequences of tokens in a similar manner as the regex language is designed to match sequences of characters. Differences are that GGS can also annotate the matched sequences and that a GGS rule / grammar is a Recursive Transitional Network which can be edited using a user friendly visual tool. To ease the manual building of such rules, a custom made tool was used, which classifies tagging errors and shows the precision yielded by the rules. Finally, the paper presents the results of the part of speech (POS) tagging model for a Romanian.
Mucous Cells and Their Structure on the Epidermis of Five Appendages in the Korean Flat -- headed Goby, Luciogobius guttatus (Pisces; Perciformes)

-- headed goby, Luciogobius guttatus , inhabits tidepools and river mouths, and stays under stones on the dried bottom for the duration of the low tide. To know the relationship of its respiration and habit in this fish, the epidermis of five appendages was observed. The epidermis has three layers: the outermost layer, middle layer and stratum germinativum. The outermost layer is composed of polygonal cells or rather flattened cells, and mucous cells. The unicellular mucous cells showing acid mucopolysaccharides are 11.1 to 16. 1 µµ m in mean height and in one or two rows. The middle layer consists mainly of large epidermal cells that are swollen by adjacent epidermal cells and arranged in a web -- shaped structure. The swollen cells are 12.3 to 15.2 µµ m in mean height and arranged in one to 11 layers. Since the swollen cells occupy the entire height of the epidermis, the epidermis is thick. A large number of blood capillaries are present just below the stratum germinativum. Taste buds are distributed at intervals on the surface of the epidermis. Based on these epidermal strucures, it is likely that L. guttatus utilizes cutaneous respiration in a dual respiratory systems.
A Virtual Patient Simulator Based on Human Connectome and 7 T MRI for Deep Brain Stimulation

This paper presents a virtual model of patients with Deep Brain Stimulation implants. The model is based on Human Connectome and 7 Tesla Magnetic Resonance Imaging (MRI) data. We envision that the proposed virtual patient simulator will enable radio frequency power dosimetry on patients with deep brain stimulation implants undergoing MRI. Results from the proposed virtual patient study may facilitate the use of clinical MRI instead of computed tomography scans. The virtual patient will be flexible and morphable to relate to patient-specific neurological and psychiatric conditions such as Obsessive Compulsive Disorder, which benefit from deep brain stimulation.
The fabrication, characterization and functionalization in molecular electronics

Developments in advanced manufacturing have promoted the miniaturization of semiconductor electronic devices to a near-atomic scale, which continuously follows the ‘top-down’ construction method. However, huge challenges have been encountered with the exponentially increased cost and inevitably prominent quantum effects. Molecular electronics is a highly interdisciplinary subject that studies the quantum behavior of electrons tunneling in molecules. It aims to assemble electronic devices in a ‘bottom-up’ manner on this scale through a single molecule, thereby shedding light on the future design of logic circuits with new operating principles. The core technologies in this field are based on the rapid development of precise fabrication at a molecular scale, regulation at a quantum scale, and related applications of the basic electronic component of the ‘electrode–molecule–electrode junction’. Therefore, the quantum charge transport properties of the molecule can be controlled to pave the way for the bottom-up construction of single-molecule devices. The review firstly focuses on the collection and classification of the construction methods for molecular junctions. Thereafter, various characterization and regulation methods for molecular junctions are discussed, followed by the properties based on tunneling theory at the quantum scale of the corresponding molecular electronic devices. Finally, a summary and perspective are given to discuss further challenges and opportunities for the future design of electronic devices.
Permanence of equilibrium points in the basin of attraction and existence of periodic solutions for autonomous measure differential equations and dynamic equations on time scales via generalized ODEs

It is well-known that generalized ODEs encompass several types of differential equations as, for instance, functional differential equations, measure differential equations, dynamic equations on time scales, impulsive differential equations and any combinations among them, not to mention integrals equations, among others. The aim of this paper is to establish a theory of autonomous equations in the setting of generalized ODEs. Thus, we introduce the notion of autonomous generalized ODEs as well as new classes of right-hand sides for nonautonomous generalized ODEs. Amongst the main results, we prove that one of these new classes coincide with the original class of right-hand sides introduced by Kurzweil in 1957. We also prove that autonomous generalized ODEs do not enlarge the class of autonomous ODEs with uniformly continuous right-hand sides. Motivated by this fact, we then enlarge the class of autonomous generalized ODEs so that discontinuities can be taken into account. We then introduce a more general class of autonomous generalized ODEs, in whose integral form, a Stieltjes-type integral appears. A correspondence between these equations and autonomous measure differential equations is established and several results are obtained. We mention local existence and uniqueness of solutions, continuous dependence of solutions on initial values, existence of periodic solutions and permanence of asymptotically stable equilibrium point in the basin of attraction. All these results are, then, specified not only for autonomous generalized ODEs, but also for autonomous measure differential equations and dynamic equations on time scales.
Entropy inequalities for semigroup actions

We extend Margulis–Ruelle inequality to the general setting of semigroup actions which are finitely generated either by Lipschitz continuous maps acting on a compact metric space or by smooth maps on a compact Riemannian manifold. We also discuss a few examples to illustrate the sharpness of our estimates.
Biomaterial-mediated cancer-specific DNA delivery to liver cell cultures using synthetic poly(beta-amino esters)

Liver cancer is a leading cause of cancer death. Most patients are treated by arterial injection of chemoembolizing agents, providing a convenient avenue for local treatment by novel therapies, including gene therapy. Poly(beta-amino esters) (PBAEs) were synthesized and used to form nanoparticles for non-viral transfection of buffalo rat hepatoma (MCA-RH7777) and hepatocyte (BRL-3A) lines with eGFP and luciferase DNA. Hepatoma cells were transfected with up to 98±0.4% efficacy with no measurable cytotoxicity. Hepatocytes were transfected with as high as 73±0.4% efficacy with 10±4% non-specific cytotoxicity. In contrast, positive controls (branched polyethylenimine, Lipofectamine ™ 2000, and X-tremeGENE® DNA HP) caused 30–90% toxicity in BRL-3A cells at doses required for >50% transfection. Of the 21 optimized PBAE-DNA formulations tested, 12 showed significant specificity for hepatoma cells over hepatocytes in monoculture ( P <0.05 for both percentage transfected and eGFP expression intensity). Top polymers from eGFP studies also delivered luciferase DNA with 220±30-fold and 470±30-fold greater specificity for hepatoma cells than hepatocytes. Transfections of co-cultures of hepatoma and hepatocytes with eGFP DNA also showed high specificity (1.9±0.1- to 5.8±1.4-fold more transfected hepatoma cells than hepatocytes, measured by percentage transfected and flow cytometry). By eGFP intensity, up to 530±60-fold higher average expression per cell was measured in hepatoma cells. One top formulation caused 95±0.2% transfection in hepatoma cells and 27±0.2% in hepatocytes (96±9% relative hepatocyte viability). PBAE-based nanoparticles are a viable strategy for liver cancer treatment, delivering genes to nearly 100% of cancer cells while maintaining high biomaterial-mediated specificity to prevent toxic side-effects on healthy hepatocytes.
The Effect of Medicare Part D on Guideline-Concordant Pharmacotherapy for Bipolar I Disorder among Dually Enrolled Beneficiaries

Objective— In January 2006 drug insurance coverage shifted from Medicaid to Medicare Part D private drug plans for the 6 million individuals enrolled in both programs. Beneficiaries faced new formularies and utilization management policies. It is uncertain if Part D, when compared to Medicaid, relaxed or tightened psychiatric medication management, which could affect receipt of recommended pharmacotherapy, and emergency department use related to treatment discontinuities. This study examined the impact of the transition from Medicaid to Part D on guideline-concordant pharmacotherapy for bipolar I disorder and emergency department use. Methods— Using interrupted time series and Medicaid and Medicare administrative data from 2004–2007, the authors analyzed the effect of the coverage transition on receipt of guideline-concordant anti-manic medication, guideline-discordant antidepressant monotherapy, and emergency department visits for a nationally-representative continuous cohort of 1,431 adults diagnosed with bipolar I disorder. Results— Sixteen months after the transition, the proportion of the population with any recommended anti-manic use was an estimated 3.1 percentage points higher than expected controlling for baseline trends. The monthly proportion of beneficiaries with 7+ days of antidepressant monotherapy was 2.1 percentage points lower than expected. The number of emergency department visits per month increased by 19% immediately post-transition. Conclusions— Increased receipt of guideline-concordant pharmacotherapy for bipolar I disorder may reflect relatively less restrictive management of anti-manic medications under Part D. The clinical significance of these changes is unclear given the small effect sizes. However, increased emergency department visits merit attention for the Medicaid beneficiaries who continue to transition to Part D.
Polysomnogram Changes in Marijuana Users Reporting Sleep Disturbances during Prior Abstinence

Background— Abrupt discontinuation of heavy marijuana (MJ) use is associated with self-reports of sleep difficulty. Disturbed sleep is clinically important because MJ users experiencing sleep problems may relapse to MJ use to improve their sleep quality. Few studies have used polysomnography (PSG) to characterize changes in sleep architecture during abrupt abstinence from heavy MJ use. Methods— We recorded PSG measures on Nights 1, 2, 7, 8, and 13 after abrupt MJ discontinuation in 18 heavy MJ users residing in an inpatient unit. Results— Across abstinence, Total Sleep Time (TST), Sleep Efficiency (SEff), and amount of REM sleep declined, while Wake after Sleep Onset (WASO) and Periodic Limb Movements (PLM) increased. Furthermore, quantity (joints/week) and duration (years) of MJ use were positively associated with more PLMs. Conclusion— The treatment of sleep disturbance is a potential target for the management of cannabis use disorders since poor sleep could contribute to treatment failure in heavy MJ users.
Reduced Plasma HDL Cholesterol in Hyperthyroid Mice Coincides with Decreased Hepatic ABCA1 Expression

The aim of the study was to investigate the influence of severe hyperthyroidism on plasma high-density lipoprotein cholesterol (HDL-C). Recently, it was shown in mice that increasing doses of triiodothyronine (T 3 ) upregulate hepatic expression of scavenger receptor-BI (SR-BI), resulting in increased clearance of plasma HDL-C. Here we show that severe hyperthyroidism in mice did not affect hepatic expression of SR-BI, but reduced hepatic expression of ATP-binding cassette transporter 1 (ABCA1), accompanied by a 40%-reduction of HDL-C. Sterol content of bile, liver and feces was markedly increased, accompanied by upregulation of hepatic CYP7A1, and ATP-binding cassette half-transporter ABCG5, which is known to promote biliary sterol secretion upon dimerization with ABCG8. Both control and hyperthyroid mice exerted identical plasma clearance of intravenously injected [ 3 H] HDL-C, supporting the view that severe hyperthyroidism does not affect HDL-C clearance, but rather its formation via hepatic ABCA1. ABCG5 CYP7A1. These data suggest that hepatic of counterbalanced diverting cholesterol the feces. Increased levels of neutral sterols from the in may compete with cholesterol and plant sterols of dietary origin, resulting in decreased intestinal absorption of dietary sterols
METHODS FORTHEASSESSMENT OF THE EFFECTS OF DRUGS ON CORONARY BLOOD FLOW IN MAN

The methods currently available for measurement of coronary blood flow in man are reviewed and their advantages and limitations discussed. Most of the techniques are invasive and involve cardiac catheterization. The least invasive isotope techniques are either not quantitative or involve expensive equipment not available in many centres. Two of the most suitable methods for assessing the effects of drugs on coronary flow are coronary sinus thermodilution and isotope washout curves using '33xenon or [12511]-iodo-antipyrine. The ideal technique for measuring coronary blood flow has yet to be developed.
TGFb1-induced phospholamban expression alters esophageal smooth muscle cell contraction in eosinophilic esophagitis

Background— Eosinophilic esophagitis (EoE) is a chronic antigen mediated disease characterized by esophageal eosinophilia, remodeling, and fibrosis. TGF β 1 is a central regulator of EoE remodeling and increases esophageal smooth muscle cell contraction. Objective— In this study, we aimed to understand the molecular mechanisms by which TGF β 1 could induce esophageal smooth muscle cell contraction. Methods— We used primary human esophageal smooth muscle (ESM) cells and EoE myofibroblasts (EMF) to assess the mechanisms of TGF β 1-induced contraction. We analyzed the expression, phosphorylation, and function of phospholamban (PLN), a sarcoendoplasmic reticulum regulatory protein which was induced by TGF β 1. Expression of PLN, phospho-PLN, and its regulatory pathway was analyzed in the esophageal smooth muscle of EoE and control biopsies. Gene silencing in EoE EMFs was utilized to understand the role of PLN in contraction. Results— TGF β 1 induced and phosphorylated PLN in primary human ESM and EoE EMFs. PLN and phospho-PLN were elevated in EoE as compared to control subject smooth muscle in vivo . PLN inhibition significantly diminished TGF β 1 induced EoE EMF contraction. PLN expression and ESM/EMF contraction depended on TGF β receptor I signals. Conclusion— We describe a previously unrecognized mechanism for esophageal smooth muscle cell contraction that depends on TGF β 1, its receptors, and PLN. Since PLN is elevated in EoE smooth muscle and PLN silencing diminishes contraction, we provide a novel potential mechanistic framework and therapeutic target for esophageal smooth muscle dysfunction in EoE. cells in vitro (10, 25). In order to understand EoE pathogenesis and elucidate novel TGF β 1 mechanisms, we utilized primary ESM and EoE myofibroblasts (EMF) to demonstrate that the contraction associated protein, phospholamban (PLN) is a TGF β 1 transcriptional target. PLN is required for proper cardiac muscle contraction and human PLN mutations can be lethal (28, 29). However, its role in EoE, in esophageal smooth muscle function and its induction by TGF β 1 has not been previously appreciated. We show for the first time that TGF β 1 induces and phosphorylates PLN in ESM cells and EoE EMFs. EoE subjects had significantly higher PLN and phospho-PLN expression in the esophageal smooth muscle in vivo as compared with normal control subjects. PLN down-regulation decreased TGF β 1-mediated contraction. PLN induction required the canonical TGF β 1 signaling pathway. As such, our findings reveal that PLN is a novel and previously unrecognized TGF β 1 target that likely alters esophageal smooth muscle function in the process of EoE associated tissue remodeling.
Inflammatory and Cardiac Biomarkers are Differentially Expressed in Chagas Disease

Background— Chagas disease has a long clinically silent period following Trypanosoma cruzi infection and before development of overt clinical pathology; detectable biomarkers of infection and pathogenesis are urgently needed. We tested 22 biomarkers known to be associated with cardiomyopathy to evaluate if a biomarker signature could successfully classify T. cruzi seropositive subjects into clinical Chagas disease stage groups. Methods— This cross-sectional retrospective case-control study enrolled T. cruzi seropositive blood donors (BD) that were further characterized as having chronic Chagas cardiomyopathy (CC-Correspondence: BD) or not (nonCC-BD) and seronegative (SN) control donors; we also included clinically diagnosed Chagas cardiomyopathy (CC-P). All subjects underwent a health history questionnaire, medical examination, electro- and echocardiograms (ECG and Echo) and phlebotomy. Biomarkers were measured on blinded samples by luminex bead array and Ortho VITROS. Results— A clear biomarker pattern was observed only in more severe cardiac disease; this pattern included significantly elevated levels of inflammatory cytokines IFN- γ IL-6, IL-10 and TNF- α and soluble cardiovascular disease biomarkers CK-MB, troponin, myoglobin, VCAM and NTproBNP while there were lower levels of MPO, PAI-1, and MCP-1. The markers determined to be most predictive of disease by ROC curve analysis were NTproBNP and T. cruzi PCR status. Conclusions— Although many biomarkers demonstrated increased or decreased concentrations among the clinical forms of Chagas disease, NTproBNP and T. cruzi PCR were the only tests that would independently be of clinical value for disease staging, in concert with ECG, Echo and clinical assessments. γ (p=0.005), NTproBNP (p=0.01) and troponin (p=0.005); MPO inversely correlated with parasitemia (p=0.01). We next analyzed the biomarkers in relation to cardiac measurements known to be associated with Chagas disease. We found that there were negative correlations between EF and log-transformed biomarkers including adiponectin (p=0.006), IL-10 (p<0.005), IL-6 (p=0.009), NTproBNP and troponin (both p<0.005). There were also biomarkers that had positive correlations with EF including PAI-1 (p<0.005) and SAP (p=0.02). There were positive correlations between ECG QTc and biomarkers including adiponectin (p=0.02), CRP (p=0.01), myoglobin (p=0.005), NTproBNP and troponin (both p<0.005). We also found positive correlations between ECG QRS duration and IL-10 (p=0.003), myoglobin (p=0.003), NTproBNP and Troponin (both p<0.005) with negative correlations between ECG QRS duration and biomarkers PAI-1 (p<0.005) and SAP (p=0.005).