Miracle-dz/UniFAR-FTUs huggingface dataset:
Meteo and Hydrodynamic Measurements to Detect Physical Processes in Confined Shallow Seas

Coastal sites with typical lagoon features are extremely vulnerable, often suffering from scarce circulation. Especially in the case of shallow basins subjected to strong anthropization and urban discharges, it is fundamental to monitor their hydrodynamics and water quality. The proper detection of events by high performance sensors and appropriate analysis of sensor signals has proved to be a necessary tool for local authorities and stakeholders, leading to early warning and preventive measures against environmental degradation and related hazards. At the same time, assessed datasets are not only essential to deepen the knowledge of the physical processes in the target basin, but are also necessary to calibrate and validate modelling systems providing forecasts. The present paper aims to show how long-term and continuous recordings of meteorological and hydrodynamic data, collected in a semi-enclosed sea, can be managed to rapidly provide fundamental insights on its hydrodynamic structure. The acquired signals have been analyzed in time domain, processed and finally, correlated. The adopted method is simple, feasible and easily replicable. Even if the results are site-dependent, the procedure is generic, and depends on having good quality available data. To show how this might be employed, a case study is examined. In fact, it has been applied to a coastal system, located in Southern Italy, where two monitoring stations are placed in two interconnected basins. The inferred results show that the system is not wind dominated, and that the annual trends in the wind regime, wave spreading and current circulation are not independent, but rather reiterate. These deductions are of great interest as a predictive perspective and for numerical modelling.
Compiler orchestrated prefetching via speculation and predication

This paper introduces a compiler orchestrated prefetching system as a unified framework geared toward ameliorating the gap between processing speeds and memory access latencies. We focus the scope of the optimization on specific subsets of the program dependence graph that succinctly characterize the memory access pattern of both regular array-based applications and irregular pointer-intensive programs. We illustrate how program embedded precomputation via speculative execution can accurately predict and effectively prefetch future memory references with negligible overhead. The proposed techniques reduce the total running time of seven SPEC benchmarks and two OLDEN benchmarks by 27% on an Itanium 2 processor. The improvements are in addition to several state-of-the-art optimizations including software pipelining and data prefetching. In addition, we use cycle-accurate simulations to identify important and lightweight architectural innovations that further mitigate the memory system bottleneck. In particular, we focus on the notoriously challenging class of pointer-chasing applications, and demonstrate how they may benefit from a novel scheme of it sentineled prefetching. Our results for twelve SPEC benchmarks demonstrate that 45% of the processor stalls that are caused by the memory system are avoidable. The techniques in this paper can effectively mask long memory latencies with little instruction overhead, and can readily contribute to the performance of processors today.
A Heuristic Algorithm for a Low Autocorrelation Binary Sequence Problem With Odd Length and High Merit Factor

A low autocorrelation binary sequence (LABS) problem is a hard combinatorial problem and its solutions are important in many practical applications. Till now, the largest best-known skew-symmetric sequence with merit factor greater than 9 had a length of 189. In this paper, a new heuristic algorithm is presented for the LABS problem. The proposed algorithm stores promising solutions and this mechanism enables the algorithm to perform local searches on these solutions in a systematic way. Our algorithm was tested on skew-symmetric sequences and the obtained results are compared with results of the state-of-the-art algorithms. The proposed algorithm was able to find some new best-known skew-symmetric solutions with merit factor greater than 9 in sequence lengths over 200. The obtained results improve the suggestion from 1985 (Beenker et al.) and 1987 (Bernasconi) greatly, where the merit factor is approximately equal to 6 for long skew-symmetric sequences with length up to 199. Now, the largest best-known skew-symmetric sequence with merit factor greater than 9 has the length 225. Additionally, now all merit factors are greater than 8.5 on the interval from 159 up to 225 for odd lengths.
State estimation for networked systems: an extended IMM algorithm

In this article, the problem of state estimation for networked systems (NSs) with three kinds of observation uncertainties (i.e. missing measurements, packet delays and packet dropouts) and without timestamps in the measurement data is investigated. Both the measurement state and network transmission state are assumed to follow a Markov process, which can capture the temporal correlation nature of the measurement process and network channels. The NS is modelled as a special Markovian jump linear system (MJLS). Then, by modifying the widely adopted interacting multiple models (IMM) algorithm, an extended IMM algorithm for the state estimation of the MJLS is proposed. The multiple filters strategy adopted in this article takes advantage of the particular characteristics of each mode as much as possible and updates the probability estimation of each mode; ultimately, it achieves better estimation performance than the single filter strategy used in existing approaches. Another contribution of this article is the extension of the standard IMM algorithm to handle some special characteristics of the MJLS established herein. The effectiveness and advantage of the proposed method are verified by simulation.
Integrated microdroplet-based system for enzyme synthesis and sampling

Microdroplet-based microfluidic devices are emerging as powerful tools for a wide range of biochemical screenings and analyses. Monodispersed aqueous microdroplets from picoliters to nanoliters in volume are generated inside microfluidic channels within an immiscible oil phase. This results in the formation of emulsions which can contain various reagents for chemical reactions and can be considered as discrete bioreactors. In this paper an integrated microfluidic platform for the synthesis, screening and sorting of libraries of an organophosphate degrading enzyme is presented. The variants of the selected enzyme are synthesized from a DNA source using in-vitro transcription and translation method. The synthesis occurs inside water-in-oil emulsion droplets, acting as bioreactors. Through a fluorescence based detection system, only the most efficient enzymes are selected. All the necessary steps from the enzyme synthesis to selection of the best genes (producing the highest enzyme activity) are thus integrated inside a single and unique device. In the second part of the paper, an innovative design of the microfluidic platform is presented, integrating an electronic prototyping board for ensuring the communication between the various components of the platform (camera, syringe pumps and high voltage power supply), resulting in a future handheld, user-friendly, fully automated device for enzyme synthesis, screening and selection. An overview on the capabilities as well as future perspectives of this new microfluidic platform is provided.
Data driven coded aperture design for depth recovery

Inserting a patterned occluder at the aperture of a camera lens has been shown to improve the recovery of depth map and all-focus image compared to a fully open aperture. However, design of the aperture pattern plays a very critical role. Previous approaches for designing aperture codes make simple assumptions on image distributions to obtain metrics for evaluating aperture codes. However, real images may not follow those assumptions and hence the designed code may not be optimal for them. To address this drawback we propose a data driven approach for learning the optimal aperture pattern to recover depth map from a single coded image. We propose a two stage architecture where, in the first stage we simulate coded aperture images from a training dataset of all-focus images and depth maps and in the second stage we recover the depth map using a deep neural network. We demonstrate that our learned aperture code performs better than previously designed codes even on code design metrics proposed by previous approaches.
Optical Properties and Molar Hemoglobin Concentration of Skeletal Muscles Measured In Vivo With Wearable Near Infrared Spectroscopy

Near-infrared spectroscopy (NIRS) is a widely-used noninvasive optical technique for measuring concentration of hemoglobin species in human tissues. Despite its potential, NIRS has seen limited clinical application largely due to a lack of <italic>in-vivo</italic> standard reference. Hence, cross-validation studies to validate novel NIRS instrumentation against established NIRS devices are needed. This <italic>in-vivo</italic> study compared a wearable continuous-wave (CW-NIRS) oximeter against a non-wearable frequency-domain (FD-NIRS) oximeter on optical properties and hemoglobin concentrations. To measure absolute coefficients and stoichiometric hemoglobin concentrations, the CW-NIRS oximeter exploits spectral properties of water. Both CW-NIRS and FD-NIRS provided physiologically-valid measurements in skeletal muscles during normoxia, hypoxia, and hyperemia. Although absorption-scattering crosstalk was evident, absorption coefficient <inline-formula> <tex-math notation="LaTeX">$\mu _{a}$ </tex-math></inline-formula> and reduced scattering coefficient <inline-formula> <tex-math notation="LaTeX">$\mu '_{s}$ </tex-math></inline-formula> at 690nm and deoxyhemoglobin concentration (HbR) were mostly within agreement limits, and the measurements differed principally by a systematic offset. Specifically, CW-NIRS estimated larger <inline-formula> <tex-math notation="LaTeX">$\mu '_{s}$ </tex-math></inline-formula> values (+2 cm<sup>−1</sup>) and smaller <inline-formula> <tex-math notation="LaTeX">$\mu _{a}$ </tex-math></inline-formula> (from −0.04 to −0.08 cm<sup>−1</sup>) at all wavelengths. The results suggest that lower-cost, wearable CW-NIRS oximeters are a potential alternative to FD-NIRS to measure optical properties and molar concentration of oxyhemoglobin and HbR in skeletal muscles <italic>in-vivo</italic> as long as the estimated water content is reasonably accurate.
Matrix Confinement Plays a Pivotal Role in Regulating Neutrophil-generated Tractions, Speed, and Integrin Utilization*

Background: Neutrophils must generate well regulated forces to migrate within the confined, three-dimensional space of diseased tissues. Results: Spatial confinement induces a switch to integrin-independent motility, but integrins regulate three-dimensional traction force generation. Conclusion: Physical confinement is sufficient to induce integrin-independent motility. Significance: Spatially confined double hydrogels are a biomimetic system that may allow for ex vivo testing of neutrophil-specific therapeutics. Neutrophils are capable of switching from integrin-dependent motility on two-dimensional substrata to integrin-independent motion following entry into the confined three-dimensional matrix of an afflicted tissue. However, whether integrins still maintain a regulatory role for cell traction generation and cell locomotion under the physical confinement of the three-dimensional matrix is unknown, and this is challenging to deduce from motility studies alone. Using three-dimensional traction force microscopy and a double hydrogel sandwich system, we determined the three-dimensional spatiotemporal traction forces of motile neutrophils at unprecedented resolution and show, for the first time, that entry into a highly confined space (2.5D) is a sufficient trigger to convert to integrin-independent migration. We find that integrins exert a significant regulatory role in determining the magnitude and spatial distribution of tractions and cell speed on confined cells. We also find that 90% of neutrophil tractions are in the out-of-plane axis, and this may be a fundamental element of neutrophil traction force generation.
The Effects of Electronic Cigarette Emissions on Systemic Cotinine Levels, Weight and Postnatal Lung Growth in Neonatal Mice

Background/Objective Electronic cigarette (E-cigarettes) emissions present a potentially new hazard to neonates through inhalation, dermal and oral contact. Exposure to nicotine containing E-cigarettes may cause significant systemic absorption in neonates due to the potential for multi-route exposure. Systemic absorption of nicotine and constituents of E-cigarette emissions may adversely impact weight and lung development in the neonate. To address these questions we exposed neonatal mice to E-cigarette emissions and measured systemic cotinine levels and alveolar lung growth. Methods/Main Results Neonatal mice were exposed to E-cigarettes for the first 10 days of life. E-cigarette cartridges contained either 1.8% nicotine in propylene glycol (PG) or PG vehicle alone. Daily weights, plasma and urine cotinine levels and lung growth using the alveolar mean linear intercept (MLI) method were measured at 10 days of life and compared to room air controls. Mice exposed to 1.8% nicotine/PG had a 13.3% decrease in total body weight compared to room air controls. Plasma cotinine levels were found to be elevated in neonatal mice exposed to 1.8% nicotine/PG E-cigarettes (mean 62.34± 3.3 ng/ml). After adjusting for sex and weight, the nicotine exposed mice were found to have modestly impaired lung growth by MLI compared to room air control mice (p<.054 trial 1; p<.006 trial 2). These studies indicate that exposure to E-cigarette emissions during the neonatal period can adversely impact weight gain. In addition exposure to nicotine containing E-cigarettes can cause detectable levels of systemic cotinine, diminished alveolar cell proliferation and a modest impairment in postnatal lung growth.
Comparative study between atorvastatin and losartan on high fat diet‐induced type 2 diabetes mellitus in rats

Obesity is often associated with chronic inflammatory state which contributes to the development of insulin resistance (IR) and type 2 diabetes mellitus (T2DM). This study investigated the effects of single and combined administration of atorvastatin (ATOR, lipid‐lowering drug) and losartan (LOS, angiotensin receptor antagonist) on metabolic disorders and inflammatory status that are implicated in the development of T2DM with the use of pioglitazone (PIO) as a standard antidiabetic drug. T2DM was induced in male rats by high‐fat diet (HFD) feeding for 16 weeks. Oral administrations of ATOR (10 mg/kg), LOS (20 mg/kg), PIO (3 mg/kg), their binary combinations, or vehicle were started in the last 4 weeks. Fasting serum glucose, oral glucose tolerance, fasting serum insulin, IR, serum lipid profile, serum TNF‐α and body composition index were determined. Results showed that all drugs and their combinations had positive impact effect on all measured parameters, and better results were achieved from binary drug combinations than administration of each drug alone. Combination of PIO with either ATOR or LOS provided better improvements on T2DM‐associated metabolic abnormalities and inflammatory status with respect to each drug alone. However, the most pronounced effects of drugs and their combinations regarding the above parameters were attributed to LOS + PIO combination. In conclusion, this study indicates that combination of ATOR + PIO and, in particular, LOS + PIO can be used as promising effective therapies in the management of HFD‐induced T2DM. This concept may be attributed to the combined effects of the respective monotherapies to improve lipid profile, insulin sensitivity, and TNF‐α level.
Words, Concepts, and the Geometry of Analogy

This paper presents a geometric approach to the problem of modelling the relationship between words and concepts, focusing in particular on analogical phenomena in language and cognition. Grounded in recent theories regarding geometric conceptual spaces, we begin with an analysis of existing static distributional semantic models and move on to an exploration of a dynamic approach to using high dimensional spaces of word meaning to project subspaces where analogies can potentially be solved in an online, contextualised way. The crucial element of this analysis is the positioning of statistics in a geometric environment replete with opportunities for interpretation.
Naringenin Eye Drops Inhibit Corneal Neovascularization by Anti-Inflammatory and Antioxidant Mechanisms.

Purpose To investigate the effect of naringenin eye drops in corneal neovascularization induced by alkali (1 N NaOH) burn in mice. Methods Corneal neovascularization in the right eye of male Swiss mice was induced by alkali. Treatment with naringenin eye drops (0.08-80 μg; 8 μL of 0.01-10 g/L solution) or vehicle (saline) started 2 days before corneal neovascularization was induced and was performed twice a day. Mice were treated up until the time animals were euthanized and cornea tissue was collected for testing, which was 2, 4, and 6 hours after alkali stimulus for cytokine and antioxidant capacity measurements, and 3 and/or 7 days after alkali stimulus for the assessment of corneal epithelial thickness and neovascularization, neutrophil, and macrophage recruitment, and vascular endothelial growth factor (Vegf), platelet-derived growth factor (Pdgf), matrix metalloproteinase-14 (Mmp14), and pigment epithelium-derived factor (Pedf) mRNA expression. Results Naringenin eye drops inhibited alkali burn-induced neutrophil (myeloperoxidase activity and recruitment of Lysm-GFP+ cells) and macrophage (N-acetyl-β-D glucosaminidase activity) recruitment into the eye, decrease in epithelial thickness, and neovascularization in the cornea. Further, naringenin inhibited alkali-induced cytokine (IL-1β and IL-6) production, Vegf, Pdgf, and Mmp14 mRNA expression, and the reduction of ferric reducing antioxidant power and Azinobis-(3-Ethylbenzothiazoline 6-Sulfonic acid) radical scavenging capacity as well as increased the reduced glutathione and protein-bound sulfhydryl groups levels. Conclusions Collectively, these results indicate that naringenin eye drops are protective in alkali-induced corneal burn by inhibiting leukocyte recruitment, the proangiogenic factor expression, inflammatory cytokine production, and loss of antioxidant defenses.
5T4-Targeted Therapy Ablates Cancer Stem Cells and Prevents Recurrence of Head and Neck Squamous Cell Carcinoma

Purpose: Locoregional recurrence is a frequent treatment outcome for patients with advanced head and neck squamous cell carcinoma (HNSCC). Emerging evidence suggests that tumor recurrence is mediated by a small subpopulation of uniquely tumorigenic cells, that is, cancer stem cells (CSC), that are resistant to conventional chemotherapy, endowed with self-renewal and multipotency. Experimental Design: Here, we evaluated the efficacy of MEDI0641, a novel antibody–drug conjugate targeted to 5T4 and carrying a DNA-damaging “payload” (pyrrolobenzodiazepine) in preclinical models of HNSCC. Results: Analysis of a tissue microarray containing 77 HNSCC with follow-up of up to 12 years revealed that patients with 5T4high tumors displayed lower overall survival than those with 5T4low tumors (P = 0.038). 5T4 is more highly expressed in head and neck CSC (ALDHhighCD44high) than in control cells (non-CSC). Treatment with MEDI0641 caused a significant reduction in the CSC fraction in HNSCC cells (UM-SCC-11B, UM-SCC-22B) in vitro. Notably, a single intravenous dose of 1 mg/kg MEDI0641 caused long-lasting tumor regression in three patient-derived xenograft (PDX) models of HNSCC. MEDI0641 ablated CSC in the PDX-SCC-M0 model, reduced it by five-fold in the PDX-SCC-M1, and two-fold in the PDX-SCC-M11 model. Importantly, mice (n = 12) treated with neoadjuvant, single administration of MEDI0641 prior to surgical tumor removal showed no recurrence for more than 200 days, whereas the control group had 7 recurrences (in 12 mice; P = 0.0047). Conclusions: Collectively, these findings demonstrate that an anti-5T4 antibody–drug conjugate reduces the fraction of CSCs and prevents local recurrence and suggest a novel therapeutic approach for patients with HNSCC. Clin Cancer Res; 23(10); 2516–27. ©2016 AACR.
Proton Pump Inhibitor Use and the Risk of Chronic Kidney Disease.

IMPORTANCE Proton pump inhibitors (PPIs) are among the most commonly used drugs worldwide and have been linked to acute interstitial nephritis. Less is known about the association between PPI use and chronic kidney disease (CKD). OBJECTIVE To quantify the association between PPI use and incident CKD in a population-based cohort. DESIGN, SETTING, AND PARTICIPANTS In total, 10,482 participants in the Atherosclerosis Risk in Communities study with an estimated glomerular filtration rate of at least 60 mL/min/1.73 m(2) were followed from a baseline visit between February 1, 1996, and January 30, 1999, to December 31, 2011. The data was analyzed from May 2015 to October 2015. The findings were replicated in an administrative cohort of 248,751 patients with an estimated glomerular filtration rate of at least 60 mL/min/1.73 m(2) from the Geisinger Health System. EXPOSURES Self-reported PPI use in the Atherosclerosis Risk in Communities study or an outpatient PPI prescription in the Geisinger Health System replication cohort. Histamine2 (H2) receptor antagonist use was considered a negative control and active comparator. MAIN OUTCOMES AND MEASURES Incident CKD was defined using diagnostic codes at hospital discharge or death in the Atherosclerosis Risk in Communities Study, and by a sustained outpatient estimated glomerular filtration rate of less than 60 mL/min/1.73 m(2) in the Geisinger Health System replication cohort. RESULTS Among 10,482 participants in the Atherosclerosis Risk in Communities study, the mean (SD) age was 63.0 (5.6) years, and 43.9% were male. Compared with nonusers, PPI users were more often of white race, obese, and taking antihypertensive medication. Proton pump inhibitor use was associated with incident CKD in unadjusted analysis (hazard ratio [HR], 1.45; 95% CI, 1.11-1.90); in analysis adjusted for demographic, socioeconomic, and clinical variables (HR, 1.50; 95% CI, 1.14-1.96); and in analysis with PPI ever use modeled as a time-varying variable (adjusted HR, 1.35; 95% CI, 1.17-1.55). The association persisted when baseline PPI users were compared directly with H2 receptor antagonist users (adjusted HR, 1.39; 95% CI, 1.01-1.91) and with propensity score-matched nonusers (HR, 1.76; 95% CI, 1.13-2.74). In the Geisinger Health System replication cohort, PPI use was associated with CKD in all analyses, including a time-varying new-user design (adjusted HR, 1.24; 95% CI, 1.20-1.28). Twice-daily PPI dosing (adjusted HR, 1.46; 95% CI, 1.28-1.67) was associated with a higher risk than once-daily dosing (adjusted HR, 1.15; 95% CI, 1.09-1.21). CONCLUSIONS AND RELEVANCE Proton pump inhibitor use is associated with a higher risk of incident CKD. Future research should evaluate whether limiting PPI use reduces the incidence of CKD.
Wheezing preschool children with early‐onset asthma reveal a specific metabolomic profile

Many children of preschool age present with recurrent wheezing. Most of them outgrow their symptoms, while some have early‐onset asthma. Aim of this prospective preliminary study was to apply a metabolomic approach to see whether biochemical‐metabolic urinary profiles can have a role in the early identification of the children with asthma.